Common Shopify Profit Report Oversights and How to Avoid Them

"Shopify profit reports are confusing! I can’t trust them entirely”

If this sounds familiar, this blog is for you.

As a Shopify merchant, it’s tempting to assume that your business is thriving when your sales dashboard shows healthy numbers. 

But even the most diligent store owners can make $50,000/ month in sales and still be broke if they don’t know their true profit margins. The truth is, overlooked fees, untracked costs and misaligned reports are quietly chipping away at your profit margins.

Whether you’re already on top of it or just starting to dig your numbers, it’s always worth stepping back for a bird’s- eye view. This guide will help you spot the most common Shopify profit reporting mistakes and how tools like Bloom Profit Analytics can help you capture your true profit margins.

The Problem with Standard Shopify Profit Reporting

Shopify is a go-to choice for most businesses, given its simplicity, scalability and robust ecosystem. But industry data shows that only 5–10% of Shopify stores succeed. 

Why? Because many Shopify owners overlook key metrics that directly impact the bottom line, such as cart abandonment rates, hidden marketing and operating costs, transaction fees, and advanced product-level profitability. 

The standard Shopify profit reports provide a solid foundation for tracking basic metrics like sales, acquisition, customer behavior, and traffic. 

However, they stop at gross profit and do not account for critical hidden costs like transaction fees, inbound shipping, agency or freelancer expenses, and packaging. That means Shopify profit reports do not show you your net profit, which often leads to overstating or understating your margins without realizing it.

To make matters worse, advanced reports and filters are only available on Shopify's higher-end plans, putting them out of reach for many merchants. Manual tracking becomes nearly impossible, especially for high-volume stores, due to Shopify’s limited customization options and weak third-party integrations.

Think again. Can you really trust Shopify alone to give you a complete picture of your store's performance?

Here’s a checklist to see if you've overlooked the key metrics quietly affecting your real bottom line.

Common Oversights in Shopify Profit Reports

1. Not Including Inbound Shipping in COGS

Shopify's built-in analytics do not automatically include inbound shipping costs like freight, customs, handling, or insurance in the product cost. Unless you manually include those amounts in the "Cost per item" field for each product, your true COGS will be understated in their reports.

2. Ignoring Transaction & Gateway Fees

If you are not using “Shopify Payments” and instead rely on a third-party payment gateway (PayPal or Stripe), Shopify will charge a transaction fee for each sale apart from the gateway fee. This will be up to 2% on the Basic plan to 5% on the Starter plan, depending on your plan.  Standard reports in Shopify often miss these key details, which can blur your true margins and require manual reconciliation.

3. Overlooking Refunds and Discounts

Shopify’s profit margin reports are often used as a foundation for strategic pricing decisions like setting product prices, offering discounts, or scaling ad campaigns. Discounts, returns and refunds often don’t get factored into Shopify profitability reports properly, leaving merchants with inflated revenue figures that potentially lead to poor decisions around product performance, pricing, or return policies.

 4. Excluding Fulfillment & Packaging Costs

If you’re not using Shopify Shipping, and instead rely on third-party carriers like FedEx, UPS, or tools like ShipStation, the shipping fees and labor or service fees associated with picking, packing, labeling, and preparing orders for shipment will not show up in Shopify’s default reporting. Shopify doesn't provide a field or setting where you can manually input these costs per order. This means your reported profit margins will be higher than they actually are.

5. Hidden Marketing Costs

Shopify does provide basic marketing reports, but the standard reporting features do not provide a way to track and analyze ad spend on various external platforms (such as Google Ads, Facebook Ads, etc.). If you don't manually account for these external ad costs on Shopify (including agency or freelancer costs for outsourcing your ad campaigns), you won't be able to clearly calculate CAC or optimize your profit margins.

Too many reports spread across too many categories, right? You are not at fault, but your system is. The right tool can help you catch everything in one place.

It’s time to switch and see!  

Get Real-Time, Net Profit Analytics with Bloom

Bloom combines all your Shopify data into one dashboard: product costs, ad spend, fees, taxes, shipping and operating costs, and shows you accurate profit information in real time.

Seamlessly integrating with multiple platforms, from ad channels like Google, Meta, Pinterest, Facebook, Bing and TikTok to subscription services and shipping providers like ShipStation and ShipHero, Bloom connects the dots across your entire ecommerce operation.

What makes it even more powerful is its ability to provide SKU-level profit analytics, so you always know exactly what’s affecting your bottom line.

Bloom's goal is to take the technical hassle off your plate so you can focus on what matters most - your products and your customers.

Here’s a quick comparison to show where Shopify’s standard reporting ends and where Bloom takes over.       

Shopify vs Bloom Profit Analytics

How to Avoid These Shopify Profit Reporting Mistakes with Bloom?

Bloom’s insights are driven by the data you plug in. So, sync the tools that matter most to your store

Once your Shopify store is connected to Bloom, it seamlessly pulls data from all major platforms like Facebook Ads, Google and more, giving you real-time insights into your entire business in one unified dashboard.

Now you can see the full story behind your profits, starting with:

• Centralized Cost Inputs – Bloom pulls all your expenses into one place, giving you a unified view of costs.

• Automated Cost Tracking – Real-time cost data is automatically synced from multiple platforms, accurately calculating profit margins and reducing human error.

• Granular Profitability Monitoring – Track true profit by order, customer, product, channel, and time.

• Mobile Browser Access to Your Profits – Stay on top of your store’s performance from anywhere. (Mobile app coming soon)

What Your Profit looks like Now: with Bloom 

Let's say you sell a product for $100 on your Shopify store. 

That’s a big difference! 

This is exactly why relying solely on Shopify’s default profit reporting can give a false sense of profitability and why these hidden costs must be tracked in a more robust analytics tool like Bloom.

Conclusion

Building a brand is hard work, but turning it into a profitable business requires a strategy. To decide on a strategy, you need actionable insights, and for insights, you need a single source of truth.

As a Shopify merchant, the journey from “This is confusing” to “I’ve got it all figured out” becomes much easier when you finally have a dashboard with all your profit insights in real time. And that’s exactly what Bloom aims to do for you.

It’s hard to explain what clarity feels like until you've experienced it for yourself. That’s why we developed Bloom Analytics - to give you a taste of clarity. Plug in your store, look at your numbers and see what you’ve really been missing out.