Shopify Accounting in Canada

Shopify makes it easy to sell. It does not keep your books for you. Recording only the deposits that reach your bank can misstate your sales, your expenses and the sales tax you owe.

Figures in this guide apply to 2026 and were checked against CRA pages in September 2026.

Quick answer

Record Shopify activity at its gross amounts, not as the payouts you receive. Sales go to revenue, GST/HST (and PST or QST where you’re registered) goes to a liability account, and processing fees, refunds and chargebacks are recorded separately. A Shopify clearing account ties it together: sales flow in, deductions and payouts flow out, and the balance should return to zero once each payout is reconciled.

Key takeaways

• A payout is a net bank deposit. It is not your revenue.
• Processing fees, your Shopify subscription and app charges are business expenses. Record them; don’t let them disappear inside a net deposit.
• Sales tax you collect belongs to the government. Record it as a liability, not as income.
• Turning on taxes in Shopify does not register you with the CRA. Registration is a separate step you take with each tax authority.
• A clearing account makes every payout easy to reconcile at month-end.

Gross sales vs payouts

When customers pay through Shopify Payments, the funds are transferred to the payout bank account you set up. Before that transfer happens, other items are netted against the money you collected. Shopify’s payout details show “a breakdown of charges, refunds, adjustments, fees, and reserves,” and its exported transaction file lists an amount, a fee and a net amount for each transaction.

That is why a payout can’t be booked as revenue. If you record a $982 deposit as “sales,” you have understated your sales, left out your fees and refunds, and buried the HST you collected inside income.

Your revenue figures should come from Shopify’s sales data instead. Shopify’s finance reports cover gross sales, discounts, sales reversals and net sales, and include a Canada sales tax report. The Shopify Payments activity report shows gross activity, fees, payouts and your ending balance for a date range.

Fees, refunds and chargebacks

• Payment processing fees. Record them as an expense, such as “Merchant and payment processing fees.” Use the fee column from your payout transactions, not an estimate.
• Shopify bills. Your Shopify bill can include your subscription, app charges set by app developers, shipping labels, and transaction fees if you don’t use Shopify Payments. Record these as expenses too.
• Refunds. With Shopify Payments, the refunded amount is deducted from your next available payout. Record it against a sales returns account and reverse the related sales tax. Shopify states that the original processing fee isn’t refunded to you, so the fee stays an expense.
• Chargebacks. When a cardholder disputes a charge, the disputed amount is deducted from your next available payout, and the bank also charges a chargeback fee. Record the fee as an expense. If you win, you get the disputed amount back; whether the fee is returned depends on your country or region.

Sales tax: GST/HST, PST and QST

GST/HST you collect is not your money. The CRA treats the GST/HST amounts you collect from customers as deemed trust amounts. In your books, credit it to a “GST/HST payable” liability account. If you’re also registered for PST or QST, give each tax its own payable account so each return is easy to prepare.

Registration comes first. For 2026, you generally must register for GST/HST once you’re no longer a small supplier, which for most businesses means your taxable sales exceed $30,000 in a single calendar quarter or over four consecutive calendar quarters. You can also register voluntarily.

If you’re registered, GST/HST you pay on business expenses, such as your Shopify subscription or apps, may be recoverable as input tax credits. Our guide to how GST/HST works for small businesses explains registration, charging and input tax credits in more detail.

Using a clearing account to reconcile payouts

A clearing account is a temporary balance sheet account, often named “Shopify Payments clearing.” It sits between your sales records and your bank account.

1. Record sales and tax collected into the clearing account (debit clearing, credit sales and tax payable).
2. Record refunds, chargebacks and fees out of the clearing account.
3. When the payout reaches your bank, move it from clearing to bank.
4. Check the result. Any balance left should match payouts still in transit or reserves. If it doesn’t, something is missing.

If you also take payments through PayPal or another processor, use a separate clearing account for each. Reconciling clearing accounts fits naturally into your month-end close.

Worked example: one payout for an Ontario store

Maple Trail Goods is a small Ontario store registered for GST/HST. Ontario’s HST rate is 13%. In one payout period it sells $1,000 of products to Ontario customers, collecting $130 of HST. One $100 order is refunded, along with its $13 of HST. Processing fees on the period’s charges total $35. The fee figure is illustrative only; your actual fees depend on your plan and transactions.

The net payout is $1,130 − $113 − $35 = $982. To keep things simple, the example ignores shipping, discounts and any tax shown on fee statements.

Entry	Account	Debit	Credit
1. Sales	Shopify Payments clearing	$1,130.00
	Sales		$1,000.00
	HST payable		$130.00
2. Refund	Sales returns and refunds	$100.00
	HST payable	$13.00
	Shopify Payments clearing		$113.00
3. Fees	Payment processing fees	$35.00
	Shopify Payments clearing		$35.00
4. Payout	Bank	$982.00
	Shopify Payments clearing		$982.00
Total		$2,260.00	$2,260.00

The clearing account nets to zero: $1,130 − $113 − $35 − $982 = $0. The books now show $900 of net sales, $117 of HST payable and $35 of fees, not a single $982 “sale.” You can check HST amounts with the GST/HST calculator.

Inventory and cost of goods sold

If you hold stock, the products you buy are inventory, an asset, until you sell them. When they sell, their cost moves to cost of goods sold (COGS).

Many small stores record COGS monthly using opening inventory, plus purchases, minus closing inventory. The COGS calculator walks through that formula.

Common mistakes

• Recording payouts as sales, which hides fees, refunds and tax collected.
• Counting HST collected as income, then being short when the return is due.
• Assuming Shopify’s tax settings mean you’re registered with the CRA or a province.
• Forgetting that a refund reduces the tax you owe as well as your sales.
• Missing Shopify subscription and app charges because they’re billed separately from payouts.

Frequently asked questions

Should I record Shopify sales order by order?

Not necessarily. Many small stores record a summary entry per payout or per month, using Shopify’s sales and tax reports. What matters is that gross sales, tax, refunds and fees are each recorded, and that the clearing account reconciles.

Does Shopify file my GST/HST return?

No. Shopify says it helps with charging sales tax but doesn’t remit or file your taxes for you. Use its Canada sales tax report as a starting point, then check it against your books before you file.

Why doesn’t my payout match my sales for the same day?

A payout nets together charges, refunds, adjustments, fees and reserves, so it rarely equals one day’s sales. Shopify also notes that pending payout amounts and dates are estimates that can change. The payout details page shows which transactions each payout includes.

Related on Ronidex

• The Invoice & Payment Tracking Worksheet, a free download for tracking what you’re owed and what has been paid
• Why is my business profitable but I have no cash?, for when sales look strong but the bank balance doesn’t
• More guides for online sellers in the e-commerce hub

If you’d rather have help keeping your books, see Ronidex’s bookkeeping and accounting support.