Amazon FBA bookkeeping in Canada: how to find your real profit.

By Maaz · Evolve Financial · June 24, 2026 · 6 min read

If you sell on Amazon FBA in Canada, the most important thing to understand is this: the money Amazon deposits in your bank is not your profit. It's what's left after fees, refunds and reserves — and if you book that deposit as "sales," you have no idea what you're actually earning. Real profit comes from separating your gross sales from Amazon's fees, tracking inventory as cost of goods sold, and handling GST/HST correctly.

Here's how to set up Amazon FBA bookkeeping so your numbers tell the truth.

Why your Amazon payout isn't your profit

Every Amazon disbursement is a bundle. Inside one deposit you'll find gross sales, referral fees, FBA fulfilment fees, storage fees, advertising spend, customer refunds, and money Amazon holds back as a reserve. If you record the net deposit as revenue, every one of those costs disappears — and so does your ability to price, plan or spot a product that's quietly losing money.

How to record an Amazon settlement properly

The fix is to break each settlement into its real parts and post them to the right accounts:

• Gross sales — your actual top-line revenue, before anything is deducted.
• Amazon fees — referral, FBA, storage and advertising, each tracked as an expense so you can see what selling on Amazon really costs.
• Refunds & returns — recorded against sales, not ignored.
• Reserves — money Amazon is holding, not money you've lost. It belongs on your books as a receivable.

Do this every settlement period and your profit-and-loss finally reflects reality. For higher-volume Canadian sellers, a tool like A2X can automate the breakdown straight into your accounting software.

Inventory and COGS — the number most sellers get wrong

Your FBA inventory is an asset while it sits in Amazon's warehouse — it only becomes an expense (cost of goods sold) when a unit actually sells. Recognising COGS at the point of sale is what reveals your true gross margin per product. Skip this and your profit looks great in months you buy little stock, and terrible in months you restock — neither of which is real.

GST/HST for Amazon sellers in Canada

Since Canada's marketplace rules took effect, Amazon is treated as a "marketplace facilitator," which changes who handles the tax:

• If you're not GST/HST registered: Amazon generally collects and remits the tax on your Canadian sales for you.
• If you are registered: Amazon collects the tax and passes the GST/HST portion back to you in your disbursements — and you remit it to the CRA yourself.

Either way, you're still expected to report those marketplace-facilitated sales on your own GST/HST return. And note: storing FBA inventory in Canada can itself create a registration requirement, especially for non-resident sellers. The rules are nuanced, so it's worth confirming your exact situation — see our guide to HST registration in Ontario for the thresholds.

Keep it clean from day one

Amazon bookkeeping done right gives you something most sellers never have: a clear, per-product view of what's actually making money. That's what lets you scale the winners and cut the losers. If you'd rather not wrestle with settlement reports, our e-commerce bookkeeping service is built for Canadian Amazon and Shopify sellers.

Frequently asked questions

Do I need a separate bookkeeper for my Amazon FBA business?

If you're doing real volume, yes — Amazon bookkeeping isn't like a normal retail shop. Settlements bundle fees, refunds and reserves, and getting COGS and GST/HST right takes someone who knows the platform. A bookkeeper who understands FBA pays for themselves by showing you which products actually make money.

How do I figure out my real profit on Amazon?

Start from gross sales, then subtract Amazon's fees, advertising, refunds and your cost of goods sold for the units that sold. What's left is your real profit — usually very different from the deposit that hit your bank. Tracking it per product is where the insight is.

What happens if I don't report my Amazon sales or GST/HST correctly?

Under-reporting sales or mishandling GST/HST can mean penalties, interest and a much harder CRA review later. Even when Amazon collects the tax for you, the sales still belong on your return. Getting it right from the start is far cheaper than untangling it during an audit.