Shopify Inventory Management — The Complete Guide for Makers (2026)

Last updated: March 2026.

Shopify is genuinely excellent at what it does — getting your products in front of customers and processing orders. But Shopify inventory management? That’s a different story. The further you get into actually running a handmade business on Shopify, the more gaps you start to notice.

You can track how many finished candles are sitting in your shop. You can’t track how much soy wax you have left. You can see that an order came in for 10 lip balms. You can’t automatically deduct the beeswax and shea butter that went into making them. And at tax time? Shopify won’t help you calculate your COGS.

This guide covers exactly what Shopify’s inventory tools do, how to get more out of them with automation, and where you’ll need to bring in extra support — especially if you manufacture products from raw materials.

How Shopify’s built-in inventory management works

Shopify tracks inventory at the product variant level. Once you turn on inventory tracking for a product, it monitors stock quantities, updates counts when orders come in, and lets you know when items go out of stock.

Here’s what you get out of the box:

Inventory history — Shopify keeps 90 days of inventory history per product: what changed, when, and why (order, manual adjustment, transfer). Useful for spotting trends and catching mistakes.

Multi-location tracking — If you store stock across multiple locations (a home studio, a market stall, a fulfillment centre), Shopify lets you track quantities at each location separately. You can see total stock across all locations or drill into individual sites.

Transfers — Shopify’s transfer tool records incoming purchase orders from suppliers. When you receive the goods, your inventory updates automatically. You can mark items as fully or partially received, which is helpful if suppliers ship in batches.

CSV bulk updates — For large inventory adjustments, you can upload a CSV with updated quantities. This works for both single-location and multi-location inventory. Not glamorous, but it works.

Out-of-stock behaviour — You can configure products to stop selling when they hit zero, or to continue selling and go negative (useful if you can still fulfil from upcoming production). You can also use automated collections to hide out-of-stock items from your storefront.

That’s a solid foundation. But notice what’s missing: there’s no concept of raw materials, no bill of materials, and no cost calculation. Shopify knows you have 24 lip balms. It doesn’t know what went into making them.

Shopify plans and inventory features (2026)

Shopify’s current plan lineup (monthly pricing, annual billing saves ~25%):

The main inventory-related jump between plans is Shopify Flow — the automation tool — which is included from the Shopify plan and above. If you’re on Basic and want automated stock alerts or supplier emails, you’ll need to upgrade or use a third-party tool.

Shopify offers a 3-day free trial to test the platform before committing.

One more thing worth noting: Shopify Stocky, the app that used to add forecasting and purchase order management, was discontinued in 2026 and shut down entirely. If you see references to it elsewhere, that information is out of date.

Automating inventory tracking with Shopify Flow

Shopify Flow is the automation tool that makes a real difference for inventory management. If you’re on the Shopify plan or higher, it’s worth spending an hour setting these up.

Flow uses a trigger-condition-action model: something happens → check a condition → do something. For inventory, the most useful automations are:

Low-stock email alerts — When a variant’s available quantity drops below a threshold you set, Flow sends you (or your ops team) an email. Sounds simple, but it’s far better than manually checking your dashboard and hoping you notice before you sell out.

Automatic product tags — When stock drops below 5 units, tag it “low-stock”. When it recovers, remove the tag. Use those tags to control collections, discount eligibility, and merchandising — all without touching anything manually.

Supplier reorder emails — Store your supplier’s email address and your reorder quantity in product metafields, then have Flow automatically email them when you hit your reorder point. No spreadsheet reminders, no forgotten purchase orders.

Stockout task creation — When a product hits zero, create a task in your project management tool. Your team knows immediately, and you can start a manufacture before customers start complaining about wait times.

Ad campaign pauses — When inventory hits zero, pause the ad sets driving traffic to that product. Stop burning budget sending people to sold-out listings. When stock comes back, unpause automatically.

For a detailed walkthrough of each automation with copy-paste templates, see our full guide: Shopify Flow for Inventory — 5 Automations Every Maker Should Turn On.

The limitation worth knowing: Flow only sees finished product inventory inside Shopify. It doesn’t know about your raw materials, your production schedule, or your stock on other channels like Etsy. That matters if you’re a maker.

The gap: what Shopify inventory doesn’t cover for makers

Here’s where things get real for handmade businesses. Shopify’s inventory tools were designed for retailers who buy finished goods and resell them. If that’s your model, they work pretty well.

If you manufacture products from raw materials, you’re going to hit some walls.

No raw material tracking. Your soy wax, fragrance oils, wicks, and jars don’t exist in Shopify’s world. You know you have 36 candles — but do you know how many more you can make with the materials on hand? Shopify can’t tell you.

No bills of materials. Shopify has no concept of a recipe or formula. It doesn’t know that each Lavender Soy Candle takes 200g of wax, 15ml of fragrance, one wick, and one jar. That means no automatic material deduction when you manufacture a batch.

No COGS calculation. Cost of goods sold is the cost of the materials and labour that went into each product. Shopify tracks order revenue. It doesn’t calculate what it cost you to make each item you sold — which you need for pricing, profitability analysis, and your tax return.

Limited multi-channel inventory. If you sell on Etsy and Shopify, your total inventory is split across two platforms. Shopify only knows about Shopify. Sell your last 3 candles on Etsy? Shopify still shows 3 in stock.

These aren’t criticisms of Shopify — they just built different software for a different problem. Retail inventory is genuinely simpler than manufacturing inventory. But if you make things, you need a system that understands that complexity.

Combining Shopify with Craftybase for complete inventory management

The most effective approach for makers is using Shopify for what it’s great at — selling — and pairing it with a manufacturing inventory system for everything that happens before the sale.

Craftybase is built specifically for this. Here’s how it works alongside Shopify:

You track raw materials in Craftybase. Every ingredient, component, and supply gets its own inventory record with purchase history, supplier details, and unit costs. When you record a batch manufacture, Craftybase automatically deducts the materials used — no manual counting, no spreadsheet gymnastics.

Bills of materials connect the dots. Define your recipes in Craftybase once. From that point, every batch you make automatically updates your material inventory. Craftybase knows how much wax went into those 50 candles, and your material count adjusts accordingly.

COGS stays accurate automatically. Craftybase calculates unit costs using weighted average costing, so as material prices change, your product costs stay current. Your COGS reports for tax time are generated automatically — no end-of-year scramble to work backwards from supplier invoices.

Stock Push syncs finished goods to Shopify (and Etsy). When you complete a batch of products, Craftybase prepares inventory updates for your sales channels. You review the numbers, then push — and both Shopify and Etsy update with a single action. No more selling the same stock on two channels.

Your Shopify orders flow into Craftybase automatically. Sales sync nightly, so your Craftybase inventory stays accurate without manual data entry. If you sell on multiple channels, orders from all of them feed into the same inventory picture.

The result: Shopify handles your storefront and checkout, Craftybase handles the manufacturing and materials layer underneath, and the two stay in sync. You get accurate inventory across both platforms, real COGS for tax time, and a clear picture of what you can make with the materials you have right now.

If you’re also using QuickBooks for accounting, Craftybase works alongside both Shopify and QuickBooks — so your inventory, sales, and bookkeeping all stay connected without manual re-entry.

Frequently Asked Questions