Tax & CRA8 min read

Shopify Bookkeeping for Canadian Sellers: The Complete Guide (2026)

How to properly track Shopify revenue, fees, refunds, and GST/HST as a Canadian e-commerce seller. Stop recording net payouts as revenue. Fix your books.

VRITTI Team

Written + fact-checked by the VRITTI editorial team

Published

The #1 bookkeeping mistake Shopify sellers make

Your bank shows a $6,420 deposit from Shopify. You record it as $6,420 in revenue. You just made the most common bookkeeping error in e-commerce.

That $6,420 is not your revenue. It's the net payout — what's left after Shopify deducted transaction fees, refunds, chargebacks, and reserves. Your actual gross revenue was $6,840. The missing $420 represents legitimate business expenses that you're now invisible to your P&L, your tax return, and the CRA.

What's actually inside a Shopify payout

Every Shopify payout bundles multiple components into a single bank deposit:

ComponentExampleCategory
Gross Sales (47 orders)$6,840.00Revenue
Transaction Fees-$198.36Expense
Refunds (2 orders)-$189.00Expense / Revenue Reversal
Chargeback Reserve-$32.64Expense
Net Payout$6,420.00What hits your bank

If you record the net $6,420 as revenue, you're understating income by $420 and hiding $420 in deductible expenses. Over a year, this adds up to thousands in missed deductions.

How to properly record Shopify payouts

The correct approach is to break each payout into its components:

  1. Record gross sales as revenue — $6,840 in this example
  2. Record Shopify fees as an expense — $198.36 under "Payment Processing Fees"
  3. Record refunds as negative revenue — $189.00 reduces your gross income
  4. Record chargebacks as an expense — $32.64 under "Chargeback Losses"

Now your books show the full picture: real revenue, real expenses, and a bank deposit that reconciles perfectly.

GST/HST for cross-province Shopify sales

If you sell to customers across Canada, tax gets complicated. The key rule: tax is based on the buyer's province, not yours.

If you're based in Alberta (5% GST) and ship to Ontario (13% HST), you charge 13% HST on that sale. If you ship to Nova Scotia, it's 15% HST. If you ship to Quebec, it's GST + QST (14.975% combined).

Shopify automatically calculates the correct tax at checkout if you've set up your tax settings properly. But you still need to track how much tax you collected per province for your GST/HST return.

Automate the whole thing

VRITTI connects directly to the Shopify Payouts API and automatically breaks down every payout into gross sales, fees, refunds, and chargebacks. Each component becomes a separate, properly categorized transaction in your books.

It also calculates destination-based GST/HST for cross-province sales and summarizes your tax collected by province — ready for your CRA filing.

No more manual reconciliation. No more paying A2X $40/month on top of your bookkeeping app. One app, $24/month, built for Canadian sellers.

Try VRITTI free for 14 days →

Frequently asked questions

Should I record the Shopify payout or the gross sale as revenue?

Always record the gross sale as revenue and the Shopify fees as a separate business expense. Recording the net payout as revenue understates your gross income and hides your fee expenses, which can cause issues with CRA and make your P&L inaccurate.

What Shopify fees can I deduct as a business expense in Canada?

All Shopify fees are deductible business expenses: subscription fees ($39-399/mo), transaction fees (0.5-2%), payment processing fees (2.4-2.9% + $0.30), app subscription fees, and theme purchases. Track each category separately for clean tax filing.

Do I charge GST/HST on Shopify sales to other provinces?

Yes. GST/HST is destination-based in Canada. If you ship from Alberta (5% GST) to Ontario, you charge the buyer 13% HST. If you ship to Nova Scotia, you charge 15% HST. You must track the correct rate per order for accurate CRA filing.

What is the best Shopify bookkeeping app for Canadian sellers?

VRITTI is built specifically for Canadian Shopify sellers. It breaks down every payout into gross sales, fees, refunds, and chargebacks. It calculates destination-based GST/HST for cross-province sales and includes a Tax Jar that shows exactly what to set aside for CRA.

Your starting point is valid

Finally safe to look.

VRITTI starts with how you feel about money — not how much you have. Financial wellness with emotional onboarding, shame-free challenges, and a 16-module Academy.

Join the waitlist — free

More guides