Shopify does a decent job tracking what you sell and how many units you have on hand. What it doesn’t do well is track what those products actually cost you from an accounting perspective. The number you see in Shopify as “cost per item” is a static field. It doesn’t automatically adjust for shipping costs to receive inventory, duties, packaging materials, or changes in supplier pricing over time. For proper bookkeeping and accurate tax reporting, you need more than what Shopify gives you out of the box.

The foundation is connecting Shopify to an accounting system like QuickBooks Online. Apps like A2X or Webgility pull your Shopify sales data into QuickBooks and break it down into revenue, fees, shipping collected, taxes, and cost of goods sold. This matters because Shopify deposits a lump sum into your bank account after deducting their fees. Without a tool parsing that data, you’re left trying to reconcile a single bank deposit against dozens or hundreds of individual orders.

On the purchasing side, every time you buy inventory from a supplier, that purchase needs to be recorded in QuickBooks with the actual cost per unit. Include freight charges, customs duties if you’re importing, and any other costs to get the product to your warehouse or fulfillment center. These are called landed costs, and they’re part of your true inventory cost. Ignoring them means your profit margins look better on paper than they actually are.

Pick a costing method and stick with it. Most small Shopify sellers use either FIFO (first in, first out) or weighted average cost. FIFO assumes the oldest inventory gets sold first. Weighted average recalculates your cost per unit each time you receive new stock. Either method works, but you need to be consistent because switching methods creates problems with the IRS and makes your year-over-year numbers unreliable.

Do regular inventory counts. Even if you’re using a 3PL or fulfillment center, the counts they report don’t always match what your books show. Shrinkage, damaged goods, returns that get restocked at a different value, and miscounts all create discrepancies. Reconciling physical counts against your accounting records at least quarterly keeps your inventory valuation honest and your cost of goods sold accurate.

Returns deserve attention too. When a customer returns a product, the cost of that item needs to go back into inventory if you’re reselling it. If it’s damaged and gets written off, that’s a different entry. Shopify processes the refund on the sales side, but the inventory accounting side needs to reflect what actually happened to the product.

The goal of all this tracking is knowing your real margins. Not your Shopify dashboard margins, which ignore half your costs, but your actual profit after accounting for what you paid for products, what it cost to get them to your door, and what you lost to returns and damaged goods. That number is what matters when you’re deciding whether to reorder a product, run a promotion, or raise prices.

If your books are behind or your inventory numbers don’t match reality, a small business bookkeeping service familiar with e-commerce can get your accounts cleaned up and build a system that keeps inventory costs accurate going forward. The longer inventory discrepancies go unaddressed, the harder they are to untangle at year end when your accountant needs reliable numbers for your tax return.