If you sell on Amazon or Shopify, you have lived this moment: you check your payout and it is hundreds of dollars less than your sales. Your first thought is that something went wrong. Usually, nothing did. Three normal mechanics explain the gap — and understanding them is the difference between clean books and a tax-season mess.

1. Fees come out before you get paid.
Amazon takes referral fees (typically 8–15%), plus FBA and shipping fees; Shopify takes its subscription and per-transaction cut. What lands in your account is the net amount. But the CRA taxes you on the gross sale — the full amount the customer paid, not what reached your bank. If your books only record the deposit, you are understating your income.

2. Payouts ignore the calendar.
Marketplaces pay on their own schedule, often 7–14 days after the sale. A payout that arrives on October 3 can easily include September sales. Without matching each payout to its sales period, your monthly numbers — and your HST return — drift out of shape.

3. Refunds and adjustments are netted silently.
A customer return, a chargeback, or a fee adjustment simply shrinks the next payout. The settlement report lists every line; your bank statement does not. A wrongly charged fee is invisible unless you reconcile.

What to do about it

• Download the monthly settlement report from Seller Central or your Shopify admin. It is the only complete record of what happened.
• Reconcile every payout: gross sales minus fees minus refunds should equal the deposit. If it does not tie, investigate.
• Record fees as their own expense line. They are deductible, and burying them inside cost of goods hides money you could claim.
• Track HST/GST by the buyer’s province, not yours. Marketplace sales cross provincial lines, and the rate follows the customer.

Doing this by hand every month is exactly the kind of work that piles up until tax season. TFB Tax & Bookkeeping’s e-commerce bookkeeping for Shopify and Amazon sellers — from $399/month — handles payout reconciliation, fee tracking, HST across provinces, and a monthly profit report. All on QuickBooks Online, by a QuickBooks ProAdvisor.

FEIFEI 437-879-6899 | taxfinbiz.com/ecommerce-bookkeeping/