4 Common Shopify Inventory Issues and How to Fix Them

Shopify inventory issues for growing manufacturers typically fall into four categories: no raw material tracking, no reorder alerts, missing batch and lot traceability, and limited reporting.

To fix them, you'll need to either extend Shopify with inventory management apps or integrate a dedicated manufacturing platform.

Here's how to identify each issue and solve it.

Shopify is mainly used by drop shippers and resellers. So if you're a manufacturer or own a growing workshop, you're likely running into Shopify inventory management issues that the platform wasn't designed to handle.

The features are built for resellers and drop shippers — not for manufacturers who need to manage production, purchasing, and multi-level inventory.

Shopify lets you create an unlimited number of products, though it becomes difficult to manage once you pass 500 products due to limited filtering and searching. It also has a POS system for brick-and-mortar stores and reports for some basic KPIs.

But what about raw materials? Purchasing? Vendor management? Production? Reordering? Advanced inventory reports? Profit margin? Bills of materials?

In these areas, Shopify falls short.

Here are the four most common Shopify inventory issues — and how to solve each one.

1. Raw material inventory management

Shopify's inventory features are geared toward resellers and drop shippers. It will tell you the "incoming stock" you've purchased and even give you the option to stop selling a product when you're out of stock.

Those are decent options for a simple operation. But what if you're a growing bike shop that builds custom bikes? How do you track all the components that go into each one?

Shopify has no raw materials inventory tracking. You'd have to manually track the purchase of raw materials on a separate spreadsheet, update it by hand as you consume materials, and then update Shopify again when the finished bike is ready.

That's a lot of double entry. And it only gets worse as your product catalog and raw material list grow. Many of these steps are repetitive tasks that eat up hours every week — time better spent growing your business.

Why Shopify doesn't track a bill of materials

If you've searched for "Shopify bill of materials," you already know the answer: Shopify doesn't support BOMs natively. There's no way to define which raw materials or components make up a finished product inside Shopify. For manufacturers and assemblers, this is one of the biggest gaps.

A proper bill of materials lets you define every component, sub-assembly, and raw material that goes into a finished good — along with quantities. Without it, you can't auto-deduct raw materials when production finishes, and you can't calculate whether you have enough stock to build what you need.

How to solve it

You need a platform that sits alongside Shopify and handles the manufacturing side. Brahmin Solutions, for example, integrates directly with Shopify and tracks all your raw materials, components, and finished goods in one place.

It can track all the variations your product has, along with every component specific to each variant — essentially creating a full bill of materials. You can see at a glance whether you have enough raw materials to produce a batch, get suggested reorder quantities, and automatically update inventory levels when production orders are finalized.

2. Reorder alerts and purchasing

Knowing when to purchase and how much to purchase is critical. Buy too little and you run out of stock to sell or produce. Buy too much and your capital is tied up in inventory sitting on shelves.

Shopify doesn't alert you when you're running low on a specific product. This is double the trouble when you consider that it doesn't track raw materials either.

That means you're left to visually scan your inventory list and filter manually. If you've tried Shopify's filtering and search for this purpose, you know it's not built for it. Manually checking inventory levels is tedious and error-prone. As a business owner or operations manager, you have far more important things to do.

Shopify inventory management challenges with multi-channel reordering

The reorder problem gets worse when you sell on multiple channels. If you're fulfilling orders from Shopify, a wholesale channel, and maybe Amazon or a B2B portal, your stock levels change constantly. Without automated reorder points, you'll find yourself overselling on one channel while stock sits unused on another.

Competitors that rank for Shopify inventory topics consistently point to multi-channel sync as a top pain point. Shopify's built-in tools don't centralize inventory across channels in a way that triggers smart purchasing decisions.

How to solve it

A dedicated inventory management system can automate reordering in several ways:

Min/max reorder points — Set a minimum threshold for each product. When stock hits that level, the system alerts you and suggests a vendor, quantity, and estimated lead time based on previous orders. Select the items to reorder, click "reorder," and purchase orders are created automatically.

Reorder from production orders — Create purchase orders for all the components of a production run, or just the items you're short on.

Make-to-stock triggers — If you produce finished goods to stock, set min/max levels for those products too. When finished goods hit the minimum, the system can automatically generate production orders so you always have enough on hand.

As stock is purchased, received, and produced, a connected platform updates inventory levels in Shopify in real time.

Want real-time visibility into every SKU? See how Brahmin tracks inventory across all your channels →

3. Batch, expiry, and serial tracking

If you're a food and beverage company, a medical device manufacturer, or an electronics company, you deal with recalls, returns, and compliance requirements that standard Shopify inventory simply doesn't support.

As a growing business that needs to batch-track, expiry-track, or serial-track inventory, you're most likely managing it all on spreadsheets. You update them manually when a specific batch or serialized product is sold. When a recall happens, you have to combine multiple spreadsheets to figure out when you bought the product, from whom, and who you sold it to — or what production run it was part of.

Shopify's inventory management comes up short here. The platform treats every unit of a SKU as identical. There's no concept of lot numbers, batch codes, or expiration dates.

What "inventory not tracked" means in this context

If you've seen the "inventory not tracked" status on a Shopify product, it means Shopify isn't managing stock levels for that item at all. For some businesses, that's intentional — for instance, digital products or made-to-order items where stock levels don't apply.

But for manufacturers, this status often signals a deeper problem: Shopify can't track what it doesn't understand. Lot-tracked or batch-tracked products need attributes that Shopify doesn't offer natively, which is why many manufacturers end up turning off Shopify inventory tracking entirely and managing everything offline.

That's a risky approach as you scale. You lose visibility, increase compliance risk, and make recalls far more painful than they need to be.

How to solve it

You need lot tracking software that connects to your Shopify store. The right platform lets you track batches, expiry dates, and serial numbers all from one place. You can pull up a specific batch, see what batches are expiring soon so you can sell them first (FIFO), and assign a specific batch or expiry date to a customer based on their requirements.

When recalls happen, you can see the complete batch history — from raw material supplier to finished product customer — within seconds. That's the difference between a minor inconvenience and a compliance nightmare. Learn more about lot numbers and how they work.

4. Reports and analytics

You want to know the number of sales per day, week, or month? You can pull those reports in Shopify, no problem. But what about profit margin? What about true profitability?

You can get an estimate in Shopify, but the cost of a product changes over time. Unless your product cost is perfectly consistent, you won't be able to track the true cost of goods sold or actual profit margin. Businesses need accurate margin data to ensure they're pricing correctly. A company's true worth is in its profitability.

Shopify inventory reports — what's missing

If you've searched for better "Shopify inventory reports," you've probably noticed the gaps. Here's what Shopify doesn't offer natively:

Without these reports, you're making purchasing and pricing decisions with incomplete information.

How to solve it

Imagine being able to see your margin on every order — and on every line item within that order. When prices change, the margin recalculates automatically. You can compare margins across different price lists and make sure your pricing meets your profitability standards.

A connected inventory platform also gives you:

Transaction report — every inventory movement, in and out

Inventory status report — incoming, in production, available, committed, and on hand

Inventory valuation — total asset value by brand, category, or location

Vendor performance — pricing history and lead-time tracking per vendor

Sales reports — by month, year, day, customer, or sales rep

Your inventory is an asset. You need to know its value at all times for accurate financial reporting. Not knowing how much inventory you have or what it's worth can lead to wasted capital and missed opportunities. If you're tracking total manufacturing costs, your reporting needs to go deeper than what Shopify provides.

Shopify inventory issues at a glance

Here's a quick summary of where Shopify falls short and what to look for in a solution:

More than just Shopify inventory issues

You see the benefits of Shopify for eCommerce, but if you're a growing manufacturer, you need more from your inventory system.

As you start processing 50+ orders a month and managing raw materials alongside finished goods, a dedicated platform becomes essential. Consider adding a manufacturing-focused system if any of the following apply:

You're managing multiple spreadsheets to track inventory

You need to track raw materials and components

You're struggling to purchase the right amount of stock

Your inventory is managed by a 3PL and needs a system to connect with them

You're looking to expand into wholesale or B2B eCommerce without paying extra for Shopify Plus

You're managing orders from multiple channels

You need to track landed costs

You're managing serialized or batch-tracked products via Excel

Frequently asked questions

Why doesn't Shopify track raw materials or components?

Shopify was built for resellers and drop shippers, not manufacturers. It tracks finished goods inventory but has no concept of a bill of materials, raw material consumption, or component-level stock. If you assemble or manufacture products, you need a separate platform that handles BOM management and syncs with Shopify.

Can I stop Shopify from tracking inventory on certain products?

Yes. You can set individual products to "inventory not tracked" in Shopify's product settings. This is useful for made-to-order items, digital products, or services. However, if you're turning off tracking because Shopify can't handle your lot or batch requirements, you're better off connecting a dedicated inventory management system rather than losing visibility entirely.

What's the best way to handle Shopify inventory for multiple sales channels?

Shopify's native multi-channel support is limited. The best approach is to use a centralized inventory platform that syncs stock levels across Shopify, wholesale, Amazon, and any other channel in real time. This prevents overselling and gives you a single source of truth for purchasing decisions.

How do I get better inventory reports out of Shopify?

Shopify's built-in reports cover basic sales data but don't include profit margin per order, inventory valuation, or inventory turnover. To get those reports, you'll need a connected platform that tracks the full inventory lifecycle — from purchase order to sale — and calculates true cost of goods sold.

How Brahmin Solutions can help

Brahmin Solutions is a cloud-based manufacturing ERP for growing manufacturers doing $500K–$50M in revenue. It integrates directly with Shopify and handles everything the platform doesn't — raw material tracking, production planning, lot traceability, automated purchasing, and the reports you actually need to run your business.

If you're outgrowing spreadsheets and Shopify's native inventory tools, book a demo and see how it fits your operation.