Shopify inventory issues for growing manufacturers typically fall into four categories: no raw material tracking, no automated reorder logic, no batch or expiry tracking, and reports that don't show real margins. (For a broader operations comparison, see our guides to the best MRP software for manufacturers, food and beverage MRP, and cosmetics MRP.)
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.
Where Shopify falls short — and for whom
The honest answer to "is Shopify enough for inventory?" depends on what you sell, where you sell it, and whether you make it.
Industries that hit Shopify's inventory wall fastest: CPG, food and beverage, supplements and nutraceuticals, cosmetics and skincare, and any operation that runs production. These industries need lot traceability, batch and recipe management, expiry tracking, and production planning — none of which Shopify ships natively. Apparel and most pure-resale DTC brands can stay on Shopify alone for much longer because they're not running production and don't need lot-level tracking.
The misconception we hear most: prospects assume Shopify is an inventory and operations system. It isn't. Shopify is a direct-to-consumer ecommerce and marketing platform — a website builder with a checkout. It's excellent at that. It is not built to manage purchasing, production, multi-warehouse stock, wholesale orders, or shop-floor workflows. When growing brands force Shopify into the operations role, they end up with spreadsheet workarounds and inventory that's always out of sync.
The trigger triad that breaks Shopify-only operations:
- Multi-channel selling. Shopify can sync to Amazon, but the moment you add wholesale, distributors, EDI to retailers, or a B2B portal, Shopify alone can't keep stock accurate across all of them in real time. Inventory needs to be the source of truth, not the website.
- Multi-warehouse and multi-location fulfillment. Shopify Locations exists, but it's surface-level. There's no smart routing logic — orders default to your primary location even when shipping from a closer warehouse would be cheaper. There are no allocation rules to prevent overselling when the same SKU sits in three places. Transfer logic is manual, which means transfer errors create accounting discrepancies. Industry data shows multi-location operations on basic tools run 5%+ inventory discrepancies quarterly — that's cancelled orders, expedited reships, and customer service tickets every month.
- Production and purchasing. The moment you start manufacturing or doing serious purchasing (raw materials, vendor lead times, reorder logic), Shopify has nothing built for it.
If you're hitting any one of those, you've outgrown Shopify-only. If you're hitting two or three at once, you're already operating with significant manual workarounds.
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 shows a low-stock badge in the admin and surfaces a basic inventory report. Shopify Flow can automate alerts but only on Shopify Plus, and even there it doesn't handle production-driven reorders — where the trigger isn't "stock dropped below X" but "a production run is scheduled and these raw materials are needed." That means most growing brands on standard plans are left to visually scan their inventory list and filter manually. If you've tried Shopify's inventory page on a 200-product catalog, you know how painful it is to triage.
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?
Explore inventory management software built for manufacturers →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:
| Report Type | Shopify | What You Actually Need |
|---|---|---|
| Sales by period | ✅ Basic reports | ✅ Available |
| Profit margin per order | ❌ Estimated only | Accurate margin per line item with dynamic cost updates |
| Inventory turnover | ❌ Not available | Turnover ratio by product, category, or brand |
| Purchase history | ❌ Not available | Full lifecycle from PO to sale |
| Inventory valuation | ❌ Not available | Real-time asset value for balance sheets |
| Vendor price tracking | ❌ Not available | Compare vendor pricing and lead times |
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.
5. Bundles and kits
If you sell single units, 6-packs, 12-packs, sample boxes, mixed-flavor variety packs, holiday gift sets, or any multi-component product, you've already met Shopify's bundle problem.
Shopify Bundles (the native app) and Shopify Plus support bundle SKUs at the storefront level. That works for the customer-facing checkout — they see one product, one price, one "Add to cart" button. What it doesn't fully solve is the inventory math: components don't decrement automatically across multi-channel inventory the way a manufacturer needs, and the moment the same products sell on Amazon or wholesale, the bundle component math falls apart. Shopify decrements the bundle SKU; it doesn't reliably decrement the twelve individual finished-good units underneath across every channel.
The workarounds are bad. Either you maintain duplicate inventory ledgers in spreadsheets, or you use a Shopify bundle app that handles the decrement but doesn't handle production, raw materials, or multi-channel sync. As soon as the same products are sold on Amazon or wholesale, the spreadsheet model collapses.
How Brahmin handles bundles
The bundle lives as one Shopify SKU. Underneath, Brahmin maps it to N components. When a customer orders the 12-pack on Shopify, Brahmin sees the order, decrements the twelve individual finished-good units, and pushes the updated stock back to Shopify in real time. Same product can be sold as singles, 6-packs, 12-packs, mixed-flavor boxes, and sample kits — each as its own Shopify SKU — all running off the same component inventory underneath.
This matters most for CPG and food and beverage brands. Variety packs, multi-flavor boxes, holiday gift sets, sampler kits, and retail-ready cases are all bundle products. If you're running them through Shopify alone, your inventory is wrong every time one of them sells.
Shopify + Brahmin: layer, don't replace
The most common question we get on demos: "Do I have to leave Shopify?"
No. Customers almost never replace Shopify. Shopify stays as the ecommerce front-end — your storefront, your DTC channel, your marketing platform. Brahmin layers underneath as the operations system: real-time inventory across every channel, raw material and BOM management, production planning, purchasing, multi-warehouse, wholesale and B2B order processing, and accurate cost-of-goods that flows to QuickBooks or Xero.
The two systems sync in real time. When a Shopify order comes in, Brahmin sees it instantly and updates available stock across every other channel. When you produce a batch in Brahmin, finished goods inventory updates in Shopify the moment the batch closes. When you receive raw materials from a supplier, Brahmin tracks the lot — and when those raw materials become finished SKUs, the lot history follows them all the way to the customer that buys them on Shopify.
This is the architecture that works for growing brands: Shopify for ecommerce, Brahmin for operations. Each tool does what it's built for.
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When Shopify alone is enough
To be honest about it: there are operations where Shopify-only is the right answer.
- You're single-channel and mostly direct-to-consumer
- You connect to Amazon or one other channel but treat it as one operational unit
- You don't manufacture — you resell or drop ship
- You don't track lots, batches, or expiry dates
- You don't run wholesale or distribute through retail buyers
- You're under ~$1M in annual revenue and your team can manage stock manually for now
If that's you, stay on Shopify. Adding an operations layer before you need one creates friction without payoff. The right time to layer in inventory and manufacturing software is when you're already doing the workarounds — not before.
Shopify inventory issues at a glance
Here's a quick summary of where Shopify falls short and what to look for in a solution:
| Issue | Shopify Limitation | What to Look For |
|---|---|---|
| Raw material tracking | No support — manual spreadsheets only | BOM management, component tracking, auto-deduction |
| Reorder alerts | No low-stock notifications | Min/max reorder points, PO automation, vendor suggestions |
| Batch/lot/serial tracking | Not supported natively | Lot traceability, expiry management, recall reporting |
| Inventory reports | Basic sales reports only | Margin analysis, inventory valuation, turnover reports |
| Multi-channel sync | Limited native support | Centralized inventory across all sales channels |
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 does Shopify show "inventory not tracked" on my products?
That status means Shopify isn't actively counting stock for that product or variant. It's typically set when the "track quantity" toggle is off in product settings — common for made-to-order, drop-shipped, or service products. For physical inventory you actually need to count, "inventory not tracked" usually means the toggle was turned off by accident, the variant was created without inventory enabled, or a Shopify app overrode the setting. Re-enable tracking under the variant's inventory tab. For manufacturers, this status often signals a deeper problem: Shopify can't track what it doesn't have categories for — raw materials, work-in-progress, or batch-level finished goods.
Why is my Shopify inventory not syncing or showing wrong stock?
Inventory sync errors usually come from one of four causes: (1) a third-party app (Amazon, Faire, wholesale portal) is updating stock on a delay, (2) Shopify Locations are configured but transfer rules aren't, so stock at one location oversells while another sits idle, (3) bundles are decrementing the bundle SKU but not the components, leaving real unit-level stock wrong, or (4) someone made a manual adjustment in Shopify admin while another system pushed a different number. The fix depends on the cause. The systemic fix — for growing brands selling on multiple channels — is to make a separate inventory system the source of truth and let Shopify reflect what it shows, not the other way around.
How do I fix Shopify inventory discrepancies?
Short term: do a full physical count, reconcile against Shopify, and identify which channel or app introduced the drift. Long term: if you're seeing 5%+ discrepancies regularly, you've outgrown Shopify-as-source-of-truth. Move inventory authority to a dedicated platform that syncs to Shopify in real time and handles the workflows Shopify can't — bundles, multi-location, raw materials, production. Once Shopify is downstream of an accurate inventory system, the discrepancies stop accumulating because the source of the drift (manual adjustments, app conflicts, channel sync delays) is no longer the system of record. (Read more on the batch-level approach for food and beverage or electronic batch records for compliance-heavy operations.)
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
Shopify is built for selling, not manufacturing — and the inventory gaps show up fast once you're producing your own products. The four issues covered in this post all stem from the same root cause: Shopify doesn't know about your BOMs, your raw materials, your production runs, or your supplier lead times. It just sees finished goods counts.
Brahmin connects to Shopify with real-time inventory sync. When a Shopify order comes in, available stock updates immediately across every channel. But the connection goes deeper than basic quantity sync. Brahmin calculates available-to-sell based on your BOMs — if you have 500 bottles of lotion listed on Shopify but you're out of shea butter to make more, the system knows your real capacity isn't 500 units, it's whatever finished goods you have on hand.
When finished goods inventory drops below your reorder point, Brahmin can trigger a work order to produce more — and MRP checks whether you have the raw materials to run that production. If materials are short, it generates purchase order suggestions factoring in supplier lead times. Sales orders on Shopify are two-way: closing an order on Shopify closes it in Brahmin, and completing fulfillment in Brahmin pushes carrier and tracking information back to Shopify.
The result is that your Shopify storefront reflects what you can actually sell, not just what's sitting on a shelf. Plans start at $199/month with unlimited users — see pricing → or book a demo to see Brahmin layered on Shopify with your products and channels.
About the author
Brahm Meka is Founder & CEO at Brahmin Solutions.
