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E-commerce guide · 2026
Bookkeeping for Shopify and Amazon payouts.
The deposit in your bank account is not your revenue. It is your revenue minus fees, minus refunds, minus reserves, minus whatever the platform decided to hold back this week. Book the deposit and both your income and your expenses come out wrong — and since 2024 the CRA has the real numbers anyway.
The core problem
Gross, not net.
A $1,000 day on Shopify might land as an $897 deposit: $1,000 of sales, less $29 of payment processing, less $74 of refunds. Recording $897 of revenue is wrong three ways over.
- Income tax. Revenue is reported gross and the platform's fees are deducted as an expense. Netting understates both sides. Your profit may land near enough, but the return does not describe your business, and neither does any lender's read of it.
- GST/HST. Tax is calculated on what the customer paid, not on what the platform sent you. A return built from deposits under-reports the tax collected.
- The CRA already knows. Since the 2024 calendar year, platforms report each seller's gross consideration by quarter and the fees they charged to the CRA every January. A return built from net deposits does not agree with the data already on file.
What the entry should look like
One deposit, several lines: gross sales, shipping charged to the customer, sales tax collected, platform and processing fees as expenses, refunds and chargebacks against revenue, and any reserve or holdback as a receivable rather than a loss. The deposit is what is left. Done monthly from the payout report, it takes minutes. Done in March from a year of bank statements, it cannot be done at all.
One payout, unpacked
| Line | Amount |
|---|---|
| Gross sales | $1,000.00 |
| Shipping collected | $45.00 |
| Sales tax collected | $135.85 |
| Refunds | ($74.00) |
| Processing and platform fees | ($29.30) |
| Reserve held back | ($50.00) |
| Deposit | $1,027.55 |
Illustration only. Six numbers matter for your return; only one of them reaches your bank.
Inventory
The count the CRA expects, and the stock sellers forget.
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A count is not optional
The CRA requires a list of the goods you hold for sale at the end of each fiscal period. It feeds cost of goods sold, and cost of goods sold is most of your profit.
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Value it consistently
Either fair market value throughout, or the lower of cost and fair market value item by item. Once you choose a method you have to keep using it in later years — switching to whichever is convenient is not available.
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Count all three places
An FBA seller's stock is usually in a Canadian fulfilment centre, a US fulfilment centre and in transit. It is all yours until it sells. Counting only what is in Canada is the classic error, and it overstates cost of goods sold in the year you make it.
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Landed cost, not invoice cost
Freight, duty and non-recoverable taxes belong in the cost of the goods. Duty is a real cost of the product; the GST you paid at the border is not, if you are registered and can recover it.
Records
Six years, and kept in Canada.
Records must be kept for six years from the end of the tax year they relate to. If you file late, six years from the filing date. If there is an objection or appeal, until it is resolved or six years, whichever is later. Records about long-term property acquisitions are kept indefinitely.
The rule sellers break without noticing: records have to be kept at your place of business or residence in Canada unless the CRA gives written permission otherwise, and keeping electronic records outside Canada needs CRA approval. If your entire accounting stack is US-hosted software with nothing held here, that is worth a conversation before an auditor raises it.
A routine that works
Monthly
Pull each platform's payout and fee report, book gross, reconcile to the bank.
Quarterly
File the GST/HST return from the sales records, not the deposits. Check any US state filings.
At year-end
Count inventory in every location, agree the platform reports to your books, and confirm the gross figures match what the platform filed with the CRA.
How we run it
Bookkeeping with a person reviewing every reconciliation: payouts unpacked to gross, fees and refunds where they belong, sales tax split between what you collected and what the marketplace collected, and inventory tracked across locations.
Then the year-end, the T2 and the GST/HST return come out of the same records rather than being reconstructed from them.
Worth knowing for 2026
The Productivity Mega Deduction announced on September 15, 2026 would allow immediate expensing of most depreciable property acquired on or after that date — software, computer equipment, warehouse machinery. It is draft legislation, not law. Inventory is not depreciable property and is unaffected.
Quick answers
What sellers ask about their books.
Should I record the Shopify deposit or the gross sales?
Gross sales, with the platform and processing fees recorded separately as expenses. The deposit is net of fees, refunds and reserves. Recording the deposit understates your revenue and your expenses, and it produces a GST/HST return that cannot be reconciled to your sales.
Does the CRA see my Amazon or Shopify numbers?
For marketplace sales, yes. Since the 2024 calendar year platforms must report each seller to the CRA annually, including gross consideration by quarter and the fees charged. Sellers with fewer than 30 sales and roughly $2,800 or less for the year are excluded.
How do I value inventory for tax?
Either at fair market value throughout, or at the lower of cost and fair market value item by item, and you must keep using whichever method you choose. Include freight and duty in cost, and count stock in Canadian and US fulfilment centres and in transit.
Do you work in QuickBooks?
Yes — QuickBooks Online if that's what the store already runs on, and we can set it up if you want it. Plenty of our clients' books are kept in Excel instead, which handles payouts, fees and inventory perfectly well without another subscription. Either way a person reviews every reconciliation.
How long do I have to keep my records?
Six years from the end of the tax year they relate to, longer if you filed late or have an objection outstanding. They must be kept in Canada unless the CRA has given written permission, and electronic records held outside Canada need CRA approval.
Sources: CRA guidance on business income and Form T2125, inventory and cost of goods sold, record retention and electronic record keeping, and the reporting rules for digital platform operators. General information, not advice for your business. See also GST/HST for Shopify and Amazon sellers.
Books built from deposits?
Call 647-870-8498 or email info@ghayurtax.com. We rebuild them from the payout reports, once, and then keep them right.