21 Pain Points Shopify Store Owners Face in 2025

We research Shopify Apps every day, if you're building in this space, get our market clarity reports

Running a Shopify store isn't getting easier.

Our team spent weeks digging through Shopify Community, Reddit, Quora, HackerNews and other forums, and what we found was eye-opening. These aren't just random complaints – they're valid feedback that could help anyone build a winning Shopify app because they prove real demand exists.

This process of digging is something we do every day when we build our market clarity reports. We prioritized fresh topics and recent conversations to see which problems plague store owners today, not yesterday.

They see their Shopify Payment account being paused or disabled

Nothing kills momentum faster than having your payment processor suddenly shut down. We're talking about store owners who wake up to find their Shopify Payments account disabled, often without clear explanations or warning signs.

The frustration level here is through the roof – imagine running promotions, getting sales, and then boom, you can't actually process payments anymore. This store owner's confusion shows just how common this issue has become.

What makes this particularly painful is the lack of transparency around why accounts get flagged. Store owners report getting generic responses from support that don't explain what triggered the suspension or how to prevent it from happening again. Some merchants on Reddit share their frustration about losing thousands in potential sales during the review period.

The ripple effects are brutal too. You've got inventory sitting there, marketing campaigns running, staff to pay, and suddenly your cash flow gets completely choked off. Multiple merchants report waiting weeks for resolution.

For app developers, this represents a massive opportunity. Store owners desperately need tools that help them stay compliant, monitor their account health, and get early warnings about potential issues. The demand is clearly there, especially among dropshippers who seem particularly affected.

They struggle with setting up a Shopify store for the first time

The learning curve for new Shopify store owners is steeper than most people expect.

You'd think setting up an online store would be straightforward in 2025, but merchants are calling it confusing and overwhelming. The platform throws so many options at you right from the start – themes, apps, payment gateways, shipping zones, tax settings – that new users often feel paralyzed.

We've noticed the pain intensifies when people try to customize their stores beyond basic templates. They hit walls with liquid code, can't figure out how to arrange products the way they envision, and struggle with seemingly simple tasks like setting up proper navigation menus. This discussion shows it's not just beginners who struggle.

The documentation exists, sure, but finding the right piece of information feels like searching for a needle in a haystack. Store owners report spending days just trying to understand the basics of collections, variants, and fulfillment settings. Many end up hiring expensive consultants just to get their store functional, which defeats the purpose of DIY e-commerce.

New merchants are literally begging for help in forums.

The connectivity issues add another layer of complexity. Getting your store connected to Shop Marketplace, Instagram Shopping, or other channels isn't intuitive. There's clearly room for onboarding tools, setup wizards, or guided experiences that could turn this painful process into something manageable.

They struggle with CSV files when importing or exporting their product data

CSV imports should be simple, but they're causing major headaches for store owners trying to manage their product catalogs.

The problems start with inconsistent field formatting – this Reddit thread dives into how frustrating it gets when your spreadsheet columns don't match Shopify's expectations. You think you've got everything lined up perfectly, then the import fails with cryptic error messages. Another thread highlights how unnecessarily complicated the whole process feels.

The workflow typically breaks down when merchants try to bulk update products, migrate from another platform, or sync inventory with external systems. They export their data, make changes in Excel or Google Sheets, and then can't get it back into Shopify without losing information or creating duplicates.

Image URLs cause particular grief – one wrong character and your entire product gallery disappears.

Variant products multiply the complexity exponentially. When you're dealing with sizes, colors, and other options, the CSV structure becomes a maze of nested relationships that even experienced users struggle to navigate. We've seen merchants accidentally delete hundreds of products because they misunderstood how the handle field works.

Several apps try to address this, like Matrixify and EZ Importer, but they're not perfect solutions. They often require subscriptions for basic functionality that should arguably be native to the platform. Plus, when we score pain points by intensity in our reports, CSV issues consistently rank high because they directly impact core business operations.

They don't know how to generate consistent traffic to their online store

Traffic generation remains the number one struggle for most Shopify store owners, and the frustration is palpable across every forum we monitor. Store owners openly admit that getting visitors feels nearly impossible.

The "build it and they will come" myth dies hard when reality hits.

New store owners often burn through their savings on Facebook and Google ads without understanding targeting, conversion tracking, or customer acquisition costs. They see other stores supposedly crushing it with organic social media, try to replicate the strategy, and get crickets. The desperation in community posts tells the whole story.

What's particularly tough is that traffic strategies that worked two years ago don't work today – algorithm changes, increased competition, and rising ad costs have completely shifted the landscape. Store owners feel like they're throwing spaghetti at the wall, hoping something sticks. Even when they run promotions or sales, they wonder if they're missing some secret sauce everyone else knows.

The knowledge gap here is massive. Most store owners don't understand SEO basics, can't interpret their analytics data, and have no framework for testing different acquisition channels systematically.

This creates opportunities for apps and services that simplify traffic generation, provide actionable insights, or automate marketing tasks that currently overwhelm store owners.

They struggle with chargebacks and payment disputes that hurt their cash flow

Chargebacks are hitting Shopify store owners harder than ever, and the financial impact goes way beyond just losing the sale.

Merchants are questioning how the entire chargeback system can even be legal when it feels so stacked against them. You ship the product, provide tracking, have proof of delivery, and still lose the dispute – plus you're hit with fees on top of losing the merchandise and shipping costs. The story of a $4,200 chargeback shows how devastating these can be for small businesses.

The dispute process itself feels like fighting with one hand tied behind your back.

Credit card companies almost always side with customers, regardless of the evidence merchants provide. Store owners report spending hours gathering documentation, writing responses, and still losing 80% of disputes. Facebook groups are filled with stories of obvious fraud that still results in merchant losses.

Cash flow takes a double hit – not only do you lose the revenue, but Shopify often holds additional funds as reserves when your chargeback rate increases. Small businesses operating on thin margins can spiral quickly when hit with multiple disputes in a short period. We always start a report by digging through signals on the internet, and chargeback complaints appear everywhere we look – our team finds this intel consistently ranks as a top concern.

The opportunity for chargeback prevention and management tools is enormous, especially solutions that help merchants document transactions better upfront.

They see a lot of bot behaviors creating fake traffic on their shop

Bot traffic is polluting analytics and creating operational nightmares for Shopify store owners who can't distinguish real customers from automated scripts. Weird large abandoned carts that make no sense are just the tip of the iceberg.

These bots add hundreds of items to carts, create fake accounts, and trigger abandoned cart emails that go nowhere.

The problem escalates when bots start placing actual orders – hundreds of bot orders can overwhelm a small operation. Store owners wake up thinking they've had an amazing sales day, only to realize it's all fraudulent activity they'll need to refund. Meanwhile, their inventory systems go haywire, their conversion metrics become meaningless, and they waste money on retargeting campaigns aimed at bots.

Community discussions reveal this isn't isolated – it's happening to stores across all niches and sizes. The bots seem to be testing credit cards, scraping pricing data, or just causing chaos for unknown reasons.

What makes this especially frustrating is that Shopify's built-in tools don't effectively filter out this traffic. Store owners can't get accurate data about their real performance, which makes every business decision harder. They're essentially flying blind, unable to trust their most basic metrics.

Bot detection and filtering represents a significant opportunity for app developers, particularly solutions that can clean up analytics retroactively and prevent bot interactions in real-time.

They see their store terminated by Shopify without any valid reason given

The nuclear option – complete store termination – happens more often than you'd think, leaving entrepreneurs devastated and confused.

Store terminations often come without warning or clear explanation. One day you're running your business, the next day you're locked out completely with just a generic email citing "terms of service violations." Years of work, customer data, and business infrastructure vanish instantly.

The appeals process feels kafkaesque – store owners report sending dozens of emails, trying to call (good luck finding a phone number), and getting nothing but automated responses.

Terminated merchants describe feeling helpless as their livelihoods disappear overnight. They can't access their customer lists to notify people, can't fulfill pending orders, and can't even export their data. The lack of explanation makes it impossible to know what to avoid if they try starting over.

What's particularly scary is that many terminated stores appear to have been operating legitimately. They weren't dropshipping counterfeit goods or running obvious scams – just regular businesses that somehow triggered an algorithmic flag. The collateral damage extends to employees who lose jobs, suppliers with pending invoices, and customers with unfulfilled orders.

This creates demand for backup solutions, store monitoring tools, and services that help merchants maintain control over their business data independent of any single platform. When we build our reports, we go through all the negative reviews and this fear of platform dependency shows up consistently.

They spend a lot of time on manual inventory tracking and stock management

Inventory management on Shopify feels like it's stuck in the stone age, forcing store owners to spend hours on tasks that should be automated. The basic question of "how to manage inventory" comes up constantly because the native tools just don't cut it.

Multi-channel selling turns inventory tracking into a full-time job.

You're selling on Shopify, Amazon, maybe in-person – and trying to keep stock levels synchronized across everything manually is a recipe for overselling or dead stock. Store owners debate whether to manage inventory in Shopify or QuickBooks, which shows how fragmented the whole system is. When inventory counts are consistently way off, you know something's fundamentally broken.

The problems compound with variants and bundles – suddenly you're tracking components, finished goods, and trying to calculate how many complete products you can actually sell. Manual counts become necessary because you can't trust the system, but bulk editing products to track inventory properly requires technical workarounds.

Low stock alerts come too late, reorder points aren't intelligent, and forecasting is basically guesswork based on Excel spreadsheets that are always out of date.

Store owners waste hours every week just trying to answer "what do I need to order?" – time that should be spent growing their business. The demand for intelligent inventory management solutions is massive, especially tools that can handle the complexity of modern multi-channel commerce.

They lose significant time managing bookkeeping tasks and workflows

Bookkeeping for Shopify stores eats up an incredible amount of time that store owners never budgeted for when starting their business.

"Is there an easier way?" perfectly captures the desperation store owners feel when drowning in receipts, invoices, and reconciliations. Every sale, refund, fee, and payout needs to be tracked, categorized, and reconciled with bank statements. The question of how to simplify accounting comes up constantly because the current solutions feel like they're built for accountants, not entrepreneurs.

Shopify's reporting gives you sales data, but that's just the beginning of what you need for proper books. You've got payment processing fees, shipping costs, app subscriptions, advertising spend, inventory purchases – all coming from different sources with different formats.

Tax season becomes a nightmare of spreadsheet archaeology.

Store owners report spending entire weekends just trying to figure out their actual profit margins. Facebook groups share horror stories of missed deductions and costly mistakes from DIY bookkeeping. The integration between Shopify and accounting software like QuickBooks exists but requires constant babysitting to ensure data syncs correctly.

Many store owners put off bookkeeping until it becomes a crisis, then scramble to reconstruct months of financial data. In our reports we usually collect between 500 and 1,000+ data points about feedback signals, and bookkeeping pain consistently ranks among the top operational frustrations in our market clarity reports.

They have a strong dislike for Shopify's Support team, especially since AI

The deterioration of Shopify's customer support has become a universal pain point that unites store owners in frustration.

Venting about Shopify support has become a regular occurrence in forums. Store owners describe it as "the absolute worst", and these aren't isolated complaints – it's a chorus of dissatisfaction. The shift to AI-powered support has made things dramatically worse, with bots providing irrelevant canned responses to complex technical issues.

You'll spend hours in chat queues only to get someone who clearly doesn't understand your problem. They paste links to help articles you've already read, ask you to clear your cache for backend issues, or simply say they'll "escalate to the technical team" and disappear forever.

Community members call support "horrendously bad", which is putting it mildly.

The escalation process has become a black hole where urgent issues go to die. Everything gets escalated now, but nothing gets resolved. Store owners with payment holds, technical bugs, or account issues wait weeks for meaningful responses while their businesses suffer.

This support vacuum creates opportunities for third-party services, community-driven solutions, and tools that help store owners solve problems without relying on official support channels. The demand for real expertise and actual problem-solving is enormous.

They are not familiar with Shopify metafields

Metafields might be powerful, but they're also confusing enough to make store owners want to pull their hair out.

"I'm losing my mind on metafields" perfectly captures the frustration level here. These custom fields should let you add extra product information, but the implementation is so unintuitive that even technical users struggle. Questions on Stack Overflow about basic metafield tasks show this isn't just a beginner problem.

The documentation explains what metafields are but not really how to use them effectively in real-world scenarios.

Store owners know they need metafields for things like size charts, care instructions, or technical specifications, but actually implementing them requires diving into liquid code that looks like ancient hieroglyphics. When metafields don't work and you need help ASAP, good luck finding clear troubleshooting guides.

The problem gets worse when you're trying to use metafields with apps or in more complex scenarios like discount functions. You think you've set everything up correctly, but the data doesn't appear where you expect it, or the formatting is completely wrong. Even experienced developers struggle with the quirks of the metafield system.

This knowledge gap represents a huge opportunity for tools that simplify metafield management, provide visual interfaces for complex data structures, or offer templates for common use cases.

They often struggle with the limitations of Shopify themes

Theme limitations are forcing store owners into a frustrating box where their vision for their store constantly hits walls.

"Why do Shopify themes still feel so limiting?" is a question that resonates with thousands of merchants. You pay good money for a premium theme, thinking it'll give you flexibility, but then you realize you can't move that button, can't change that layout, can't add that feature without hiring a developer. Store owners are feeling stuck with themes that looked great in the demo but don't work for their actual products.

The customization options that do exist are often buried in obscure settings or require coding knowledge that store owners don't have. Want to add a simple feature like a size guide popup? That'll be another app subscription or a $500 developer fee.

The promise of drag-and-drop simplicity crashes into the reality of rigid structures and limited options.

Mobile responsiveness adds another layer of frustration – something looks perfect on desktop, but completely breaks on phones where most customers shop. Store owners spend hours tweaking settings, only to have updates reset their customizations or break their carefully crafted workarounds.

Page speed suffers as stores pile on apps to overcome theme limitations, creating a vicious cycle of poor performance. When building our reports we search on different places like Reddit and Stack Overflow, and theme frustrations appear consistently across all platforms because they directly impact conversion rates and brand presentation.

They receive customer threats and aggressive messages

Dealing with threatening customers has become an unfortunately common part of running an online store, and store owners feel completely unprepared for this dark side of e-commerce. How to handle threatening customers shouldn't be something new merchants need to figure out alone, but here we are.

The threats range from bad reviews blackmail to actual personal threats against store owners and their families.

Small business owners pour their hearts into their stores, so dealing with hate and negativity hits particularly hard. A simple shipping delay or product issue can escalate into aggressive emails, social media harassment, and even doxxing attempts. Store owners report losing sleep, developing anxiety, and some even consider closing their stores entirely.

The isolation makes it worse – you're sitting alone at home, reading these horrible messages, wondering if this person knows where you live since they have your return address. Shopify provides little guidance or support for these situations, leaving merchants to navigate these waters alone. Law enforcement often can't or won't help with online threats, especially across state or country lines.

There's clearly demand for tools and services that help store owners manage aggressive customers, document threats properly, and protect their personal information while running their business. Mental health support and community resources for e-commerce entrepreneurs dealing with this stress could make a real difference.

They get a lot of spam emails that clutter their business inbox daily

The spam situation has gotten completely out of control, with store owners drowning in junk emails that make running their business harder.

One merchant reports getting 5-20 spam emails daily from people claiming they'll double their revenue. These aren't just annoying – they bury legitimate customer inquiries, supplier communications, and important platform notifications. Some stores get 200+ scam bot emails in a single day.

The contact forms meant to help customers reach you become weapons for spammers. "Tons and tons of spam" flood in through these forms, and Shopify's built-in protections do almost nothing to stop it.

You'll get fake wholesale inquiries, SEO service pitches, app developers promising miracles, and mysterious "business proposals" that are obviously scams.

The mental load of sorting through this garbage every day exhausts store owners who just want to focus on serving real customers. Important emails get missed, response times suffer, and the professional email address you were so proud of becomes a source of daily frustration. Some merchants resort to constantly changing email addresses, but that creates its own problems with customer communication and brand consistency.

Anti-spam solutions specifically designed for e-commerce could solve a real problem here, especially if they could intelligently filter while ensuring legitimate customer messages always get through.

They have a strong bounce rate with visitors leaving their site immediately

High bounce rates are killing conversions, and store owners can't figure out why visitors flee their sites within seconds. Super high bounce rates have become the norm, not the exception, leaving merchants confused and frustrated.

You spend money driving traffic through ads or SEO, visitors arrive, and boom – they're gone before even scrolling.

The reasons could be anything: slow loading times, confusing navigation, overwhelming popups, or just a mismatch between what visitors expected and what they found. But without proper tools to diagnose the issue, store owners are just guessing. High traffic but low sales is a special kind of torture when you're paying for every click.

Mobile users bounce even faster, often because the mobile experience is an afterthought. Store owners focus on making their desktop site perfect, not realizing 70% of their traffic is thumbing through on phones with different expectations and patience levels.

The analytics show the problem but not the solution – you can see people leaving, but not really why they're leaving. Heat mapping tools and session recordings exist but they're expensive and time-consuming to analyze properly. Store owners need actionable insights, not more data to interpret.

We like to score pain points by intensity in our reports, and bounce rate issues score high because they directly impact revenue and make every other marketing effort less effective.

They struggle to judge which Shopify Apps are truly useful

App fatigue is real, and store owners are overwhelmed trying to figure out which tools actually help versus which ones just drain their credit cards.

Having 14 apps installed isn't unusual, but determining their actual value is nearly impossible. Store owners constantly ask what apps are absolutely essential because the app store is a jungle of overpromises and underwhelming delivery. Every app claims to be revolutionary, but most just add complexity and monthly fees.

The free trials trick you – everything seems great for 14 days, then you're locked into subscriptions you forgot about.

Apps conflict with each other, slow down your site, and create a web of dependencies that makes troubleshooting impossible. When something breaks, good luck figuring out which of your dozen apps is the culprit. Store owners report spending hundreds monthly on apps they're afraid to remove because they can't remember what each one does.

Reviews in the app store feel fake or purchased, making it hard to trust anything. An app with 4.8 stars might be terrible, while a hidden gem with 3.9 stars could transform your business. Without honest, detailed feedback from real users in similar situations, store owners are essentially gambling with their tech stack.

There's massive demand for honest app reviews, compatibility checkers, and tools that audit your existing apps to identify redundancies and unnecessary expenses.

They deal with frequent Shopify crashes, disrupting operations

System crashes and instability are costing store owners money and sanity, with frequent crashes becoming disturbingly common.

Your store works fine one minute, then suddenly customers can't check out, you can't access your admin panel, or the entire site goes down during a marketing campaign you've been planning for months. Mobile crashes are particularly problematic since that's where most shopping happens.

The randomness makes it worse – you can't predict or prevent these issues.

Store owners describe the panic of watching real-time analytics during a crash, seeing visitors unable to purchase while they frantically try to figure out what's wrong. Sites that keep crashing lose customer trust fast – shoppers won't give you a second chance if their first experience is a broken website.

Support during crashes is essentially non-existent. You're told to check status.shopify.com (which usually says everything is fine), clear your cache, or wait it out. Meanwhile, every minute of downtime represents lost sales, damaged reputation, and wasted ad spend. The platform that promised to handle the technical stuff so you could focus on selling becomes the biggest technical headache of all.

Uptime monitoring, backup solutions, and crash recovery tools could provide real value to anxious store owners who've learned they can't rely on platform stability alone.

They get burned by opaque Shopify pricing, with unexpected costs

Hidden fees and surprise charges have store owners feeling deceived by Shopify's supposedly transparent pricing structure. Getting burned by plan changes happens regularly when Shopify adjusts their pricing without clear communication about what's actually changing.

You think you're paying $39 a month, but then transaction fees, payment processing fees, app subscriptions, and theme costs pile up until you're spending hundreds.

The transaction fees are particularly frustrating – you pay for the platform, then pay again for every sale unless you use Shopify Payments (which isn't available everywhere or suitable for every business). The opacity of Shopify pricing makes it impossible to accurately forecast costs as your business grows.

Currency conversion fees, staff account fees, and advanced report fees catch store owners off guard. Features that seem basic require upgrading to higher tiers, but the differences between plans are deliberately confusing. You upgrade thinking you'll get what you need, only to discover that feature requires yet another upgrade or an expensive app.

Budget planning becomes impossible when you can't predict what Shopify will cost next month. Small businesses operating on thin margins get squeezed by fees they didn't account for, sometimes making entire business models unviable.

Tools that help merchants understand true Shopify costs, compare alternatives, and optimize their subscription stack could save businesses thousands annually.

They want to connect with other Shopify store owners for advice and support

The isolation of running an online store drives merchants to desperately seek community and peer support.

Looking for advice on organic traffic, creating their first store, or just wanting to know they're not alone – store owners crave connection with others who understand their struggles. Running an e-commerce business from your laptop can feel incredibly lonely, especially when things go wrong.

Facebook groups and forums become lifelines, with merchants forming informal support networks. Groups for Shopify beginners show how desperate people are for guidance that goes beyond generic tutorials.

Store owners want to share victories, vent about defeats, and learn from others' expensive mistakes.

The advice gap is real – every business is different, but common patterns emerge that experienced store owners could help newbies avoid. Questions about supplier relationships, customer service scripts, seasonal planning, and growth strategies need nuanced answers from people who've been there. Official Shopify resources feel corporate and detached from the daily reality of running a small business.

Community platforms, mentorship programs, and peer support tools specifically for Shopify merchants could fill this void. The demand for authentic connection and practical advice from fellow store owners is massive and largely unmet by existing solutions.

They struggle with Shopify SEO, finding it difficult to drive organic traffic

SEO on Shopify feels like trying to win a race with your legs tied together, and store owners are frustrated by the platform's limitations. Questions like "Shopify SEO?" appear constantly because merchants can't figure out why their stores won't rank.

The confusion starts with basics – does Shopify handle SEO automatically or do you need to do everything yourself?

The answer is both and neither, which leaves everyone confused. URL structures are rigid, meta descriptions get truncated weirdly, and duplicate content issues arise from collection pages that you can't properly control.

Technical SEO becomes a nightmare with limited access to robots.txt, no control over site structure, and apps that inject code that destroys page speed. Store owners looking for optimization tips find generic advice that doesn't address Shopify-specific challenges.

The platform limitations mean you're competing with WordPress sites and custom builds that have full SEO flexibility while you're stuck with whatever Shopify allows. Schema markup, international SEO, and advanced optimization techniques require expensive apps or custom development that small businesses can't afford.

SEO tools built specifically for Shopify's quirks and limitations could help level the playing field for store owners who can't afford SEO agencies but need organic traffic to survive.

They sometimes see traffic but no conversions

The special torture of getting traffic but no conversions leaves store owners questioning everything about their business.

You've solved the traffic problem – people are visiting your store – but they're not buying anything. Lots of visits but no add-to-carts suggests something's fundamentally wrong, but what? The analytics show sessions, page views, even time on site looks decent, but that conversion rate stays stubbornly at zero.

This widespread problem has store owners pulling their hair out trying everything: redesigning product pages, adjusting prices, adding trust badges, improving descriptions, offering discounts.

Nothing moves the needle.

When conversion rates stay below 1%, every possible issue becomes a suspect. Maybe the checkout process is too complicated, maybe shipping costs shock people, maybe the product-market fit is off, or maybe your traffic sources are sending the wrong audience. Without clear diagnostics, store owners throw spaghetti at the wall hoping something sticks.

The psychological toll is heavy – watching hundreds of visitors leave empty-handed makes you question whether your business idea is even viable. Conversion optimization tools that provide specific, actionable insights rather than generic best practices could help store owners turn their traffic into actual revenue.