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To reconcile Shopify transactions, match three things every month: the orders in the store, the payouts that reached your bank, and the sales and tax in your books. If gross sales less refunds and fees equals the deposits, you’re done. If it doesn’t, the gap is a refund, a fee, a timing difference or a mistake. Find it this week.
What do you reconcile each month?
Any online store creates a chain. A customer pays, the platform holds the money for a few days, then sends one deposit that covers many orders minus fees and refunds. Your bank statement shows only the last link. So you need the store’s own sales report and payout report next to the bank line. Shopify is the example here, and the same steps work for any platform that pays out in batches. We don’t cover its fees or features, and we couldn’t confirm any of them.
A month of made-up figures
Say an Ontario store sells 20 orders at $100 plus 13% HST, so each customer pays $113. One order is refunded in full. The processing fee is assumed to be 2.9% plus $0.30 per payment, which is $3.58 an order. Those figures are ours, chosen to show the method.
| Line | Amount |
|---|---|
| Gross collected, 20 orders at $113 | $2,260.00 |
| Refund, 1 order | -$113.00 |
| Fees, 20 orders at $3.58 (fee not returned, assumed) | -$71.54 |
| Expected payout | $2,075.46 |
| Net sales in your books (19 orders) | $1,900.00 |
| HST owing on those sales | $247.00 |
Check it the other way. Net sales $1,900 plus HST $247 is $2,147, less the $71.54 in fees, which is $2,075.46. Same number. That’s a reconciliation. The GST/HST calculator gives $13 of HST on each $100, so 19 sales at $13 is $247.
Why doesn’t the payout match the month?
Usually timing. A sale on the 30th often lands in a payout in the next month. Don’t force it. Keep a small “money in transit” balance and clear it when the deposit arrives. What matters is that the sale sits in the month it was made, and the deposit clears against it later.
Next most common is a refund that hit after the payout closed. Then a fee that changed. Then the odd sale paid another way, like a bank transfer or gift card, that never touches the payout at all.
How do you handle the tax side?
Take HST from the store’s tax report, not from the deposit. If a customer paid $1,130 in Ontario, the HST reverse calculator shows $1,000 of sales and $130 of HST. The tax report should show the same split by province, and it matters because rates differ. The CRA lists 13% HST for Ontario, 14% for Nova Scotia and 15% for the other Atlantic provinces, plus 5% GST in provinces without HST. For a British Columbia customer, the GST/PST calculator shows 12% combined, though it applies that rate to everything, so don’t lean on it for exempt items.
Put tax collected in a liability account. It never belongs in income, and you can’t spend it. If you’re a sole proprietor filing GST/HST annually with a December year-end, the CRA says payment is due April 30 and the return June 15. For monthly and quarterly filers, both are due one month after the period ends.
Mistakes to look for
Booking each payout as revenue is the big one, because it hides refunds and fees inside a number that looks right. The second is skipping months and trying to catch up in March. Small differences become impossible to trace by then.
Watch for gift card sales. Selling one isn’t the same as making a sale of goods, and how it’s treated for tax is something we haven’t confirmed here, so ask your bookkeeper before you record it.
Keep the exports. The CRA says business records generally stay for six years from the end of the last tax year they relate to. The profit margin calculator is a quick way to test whether the month’s numbers look sensible once fees are in.
Where the numbers come from
The order figures are invented. Rates and deadlines come from Canada Revenue Agency pages on GST/HST rates for digital and online supplies, GST/HST reporting deadlines and record keeping, read in September 2026. 2026 dates for income tax returns weren’t confirmed.
Frequently asked questions
Why doesn't my payout match my monthly sales?
Usually timing, refunds or fees. A sale on the last day of the month often pays out the next month.
Should I book payouts as revenue?
No. Book the sales at full price, the fees as an expense and use the payout only to prove the cash.
Where does HST go in the books?
In a liability account, since it's owed to the CRA and isn't income.
How often should I reconcile?
Monthly, after the payout report closes, so differences are small enough to trace.
How long do I keep the exports?
The CRA says generally six years from the end of the last tax year the records relate to.
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Information only. This page is general information, not tax, legal or accounting advice. Tax-Services.ca is an independent publisher: we don't prepare or file tax returns or offer tax services, and we have no connection with the CRA, Revenu Québec, any government or any company named on this page. Check the figures that matter with an official source or a qualified professional.