7 Costly Shopify Mistakes I Saw Every Day When I Worked at Shopify
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I spent nearly six years working at Shopify headquarters as a Product Launch Specialist. During that time, I helped hundreds of merchants get their stores off the ground — from first-time founders selling handmade candles to established brands migrating from other platforms.
After leaving Shopify and starting my own consultancy, ShopiCraft, I've seen the same mistakes come up again and again from the other side of the table. The difference is that now I get to actually fix them.
These aren't edge cases. These are the mistakes I saw daily — and they're costing store owners real money.
1. Choosing a Theme Based on How It Looks, Not How It Works
This is by far the most common one. A merchant falls in love with a theme's demo site, installs it, and then discovers it doesn't support the features they need — whether that's advanced filtering, multi-column product descriptions, or a specific layout for their collection pages.
Here's what most people don't realise: every Shopify theme demo is styled with perfect photography, curated content, and carefully chosen settings. Your store won't look like that out of the box. What matters more is whether the theme supports the functionality you actually need.
What to do instead: Before picking a theme, write down your must-have features. Do you need a mega menu? Product variant thumbnails? A quick-add button on collection pages? Age verification? Then evaluate themes against that list — not against how pretty the demo looks. If you're unsure, a quick consultation with a Shopify expert can save you hours of frustration and potentially the cost of buying a theme you'll need to replace later.
2. Installing Too Many Apps Without Understanding the Trade-offs
The Shopify App Store is incredible — there are thousands of apps that can add almost any feature to your store. But there's a cost that most store owners don't see until it's too late.
Every app you install adds JavaScript to your storefront. Some apps add a lot. I've audited stores running 25+ apps where the homepage took 8-10 seconds to load. That's not just a bad user experience — Google factors page speed into search rankings, and slow stores convert significantly worse.
The other hidden cost is subscription creep. I regularly see stores spending €200-400/month on apps, some of which overlap in functionality or aren't even being used anymore.
What to do instead: Audit your apps quarterly. For each one, ask: is this app actively contributing to revenue or saving me meaningful time? If not, remove it. For any new app, check whether the functionality can be achieved with Shopify's built-in features first. Shopify has added a huge amount of native functionality over the years — things like automatic discounts, basic email marketing, and even some automation with Shopify Flow — that many merchants don't know exist.
3. Ignoring Shopify's Built-in SEO Features
Speaking of features merchants don't know about — Shopify has solid SEO capabilities baked right in, but most store owners never touch them. I saw this constantly: stores with auto-generated page titles like "Products – My Store Name" and completely empty meta descriptions.
Every single page on your store — your homepage, collection pages, product pages, and blog posts — has editable SEO fields. These are the title and description that appear in Google search results. If you don't customise them, you're leaving free visibility on the table.
Beyond titles and descriptions, many merchants also overlook image alt text, URL handles (the slug at the end of your URLs), and their sitemap — all of which Shopify handles well if you take the time to configure them properly.
What to do instead: At minimum, write unique SEO titles and meta descriptions for your homepage, your top 5 collection pages, and your top 20 products. Use natural language that includes the words your customers would actually search for. And always fill in image alt text — it helps with both accessibility and Google Image search.
4. Setting Up Shipping Incorrectly
This one might sound boring, but misconfigured shipping settings were one of the top reasons merchants contacted Shopify support. And it's not just about getting the rates wrong — it can actually cost you sales.
Common problems I saw: shipping rates that were far too high because the merchant set up weight-based shipping but never entered product weights. Free shipping thresholds that didn't work because they were set up as a discount code rather than a shipping rate. And international shipping that was either unavailable (losing potential customers) or available everywhere with no rate adjustments (leading to massive losses on shipping costs).
What to do instead: Test your checkout. Seriously — place a test order from every country and region you want to sell to. Check that shipping rates look reasonable. Make sure your free shipping threshold is working. And if you're selling physical products, enter accurate weights for everything. Shopify's shipping calculations are only as good as the data you give them.
5. Not Setting Up Analytics and Tracking From Day One
I can't count how many merchants I spoke to who'd been running their store for months — sometimes years — without proper analytics tracking. They had no idea where their traffic was coming from, which products people were viewing but not buying, or where customers were dropping off in the checkout.
Without this data, every decision you make about your store is a guess. Should you invest more in Instagram ads or Google Shopping? Which products should you feature on your homepage? Is your checkout conversion rate normal or terrible? You can't answer any of these questions without analytics.
What to do instead: Set up Google Analytics (GA4) and connect it to your Shopify store before you launch. Enable Shopify's built-in analytics as well — the two complement each other. If you're running ads, install your Meta Pixel and any other relevant tracking pixels from day one. The data you collect in your first few months is invaluable for making informed decisions later.
6. Trying to Make Shopify Do Something It Wasn't Designed For
Shopify is an incredibly flexible platform, but it does have an intended way of working. I saw many merchants fight against this rather than work with it — often because they were trying to replicate their old platform's workflow exactly.
For example: merchants who wanted 15 product options when Shopify supports 3 (there are apps and workarounds, but the native limit exists for good reason). Merchants who wanted completely custom checkout flows on non-Plus plans. Merchants who tried to use Shopify as a booking system, a course platform, or a marketplace without understanding the limitations.
None of these are impossible — but they require either the right apps, custom development, or sometimes accepting that a different approach will work better on Shopify.
What to do instead: If you're migrating to Shopify from another platform, don't try to recreate your old store feature-for-feature. Instead, take the opportunity to rethink your approach. What are you actually trying to achieve for your customers? A good Shopify consultant can help you find the most efficient path to get there — which might be different from what you had before, but often ends up being better.
7. Launching Without Getting a Second Pair of Eyes
The most expensive mistake of all is also the most understandable. You've spent weeks or months building your store. You're exhausted. You just want to go live and start selling. So you skip the final review and hit publish.
And then a customer emails you because the "Add to Cart" button doesn't work on mobile. Or your tax settings are wrong. Or your product descriptions have typos. Or your checkout asks for a company name when you're selling directly to consumers.
These seem like small things, but they compound. Every friction point in your customer journey costs you conversions. And first impressions matter enormously — you rarely get a second chance with a customer who had a bad experience.
What to do instead: Before you launch, have someone who isn't you go through your store. Ideally someone with Shopify experience who knows what to look for. A pre-launch audit or even a one-hour consultation can catch issues that you've become blind to after staring at your store for weeks. I've done hundreds of these, and there has never been a single one where I didn't find something worth fixing.
The Common Thread
If you've noticed a pattern in these mistakes, it's this: most of them come down to not knowing what you don't know. Shopify is genuinely one of the best e-commerce platforms in the world — I wouldn't have spent six years of my career there if I didn't believe that. But like any powerful tool, getting the most out of it requires knowing how to use it properly.
That's exactly why I started ShopiCraft. After years of helping merchants from inside Shopify, I wanted to be able to work with them directly — helping build stores, fix problems, develop custom apps, and provide the kind of hands-on guidance that makes the difference between a store that just exists and one that actually thrives.
If any of these mistakes sound familiar — or if you want to make sure you're not making them — book a free intro call and let's have a chat. No hard sell, just an honest conversation about your store and where it could be better.
Daniel Perera is the founder of ShopiCraft, a boutique Shopify consultancy based in Ireland. He spent nearly 6 years at Shopify as a Product Launch Specialist and also worked at Google. ShopiCraft is a certified Shopify Partner specialising in consulting, store builds, custom app development, and theme customization.