Updated Checked by the Tax-Services.ca editorial team How we check
The best accounting software for a Shopify store in Canada is the one that gets your sales tax right, matches your payouts to your sales and lets you export six years of records. I can’t rank named products or quote prices, because none of that could be confirmed. What I can do is tell you what to test before you commit.
What should accounting software for Shopify actually do?
Forget the feature lists for a minute. Your store creates four kinds of numbers: sales, sales tax collected, refunds and the money that lands in your bank. Software earns its place when it keeps those four straight.
Ask to see each of these working with your own data, on a free trial if one exists.
- Sales tax by province. An order to Ontario carries 13% HST, one to Alberta carries 5% GST, and one to Quebec adds QST on top of GST.
- Refunds and returns that reverse the tax as well as the sale.
- Bank deposits that tie back to orders, even when the payment processor deducts its fees before paying you.
- Reports you can hand over at filing time or to an accountant.
Any package can do the plain cases. Test the messy ones.
Which sales tax rates must your books handle?
This is where most stores get into trouble. You charge tax by where the customer is, so a single store can need several rates.
| Province | Rate on most goods |
|---|---|
| Ontario | 13% HST |
| Nova Scotia | 14% HST |
| New Brunswick, Newfoundland and Labrador, Prince Edward Island | 15% HST |
| Alberta, Yukon, Northwest Territories, Nunavut | 5% GST only |
British Columbia, Saskatchewan, Manitoba and Quebec charge their own provincial tax on top of the 5% GST. The GST/HST calculator handles the first group. On a $100 sale in Ontario it shows $13.00 of HST and a $113.00 total. For Quebec, the GST and QST calculator shows $5.00 of GST plus $9.98 of QST, so $14.98 of tax. The GST and PST calculator covers the western provinces, with a warning: for BC it taxes everything at 12%, so it overstates the tax on goods that carry only GST.
Already have a tax-included price? The HST reverse calculator strips the tax out, so $113.00 in Ontario comes back to $100.00 before tax.
When do you have to register for GST/HST?
You’re a small supplier while your taxable sales stay at $30,000 or less, both in a single calendar quarter and over the last four quarters in a row. Go over and you must register. You then have 29 days from your effective date, which is no later than the day of the sale that took you past the limit if one quarter did it. If you sell to Canadians online, GST/HST applies to those sales like any other. The CRA lays this out on its page about when to register for and start charging the GST/HST.
Ask a simple thing of the software: can it show your rolling four-quarter total of taxable sales? That one report tells you when you’re getting close.
How do you test software with one real month?
Don’t judge it on the demo. Take last month’s Shopify orders and run them through the trial. Pick five awkward ones: an Ontario order, a Quebec order, a refund, a partial refund and an order where the processor held back a fee. Then check three things. Does the sales tax match what the customer was charged? Does the deposit in your bank equal sales, minus tax you’ll remit, minus fees? Can you see a refund reversing the tax?
If any of those needs a workaround you can’t explain to a friend, keep looking. An hour of testing now saves a lot of cleaning later, and a few bucks a month for the right tool is cheaper than a weekend of fixing books at tax time.
How to choose between the options
Once the basics pass, compare on things you can verify. Ask the vendor for the total cost with any add-ons, how the software connects to Shopify (a built-in link, a third-party app or a manual file), and whether you can export everything if you leave. An example is QuickBooks Online, which you can trial and judge for yourself, but I’m not claiming it beats anything else.
Also think about size. A store that sells $40,000 a year needs a simple ledger. One with staff needs payroll, and the payroll remittance calculator shows what you’d owe the CRA each period.
Margins matter more than most owners think. At a $100 price and a $60 cost you make $40 per item, a 40.0% margin, according to the profit margin calculator. Good books show that number per product after fees.
Mistakes and limits
- Don’t count sales tax as revenue. It belongs to the government until you remit it.
- Don’t rely on the software’s default rates without checking them against the CRA table.
- Don’t throw records out early. The CRA says to keep records for six years from the end of the last tax year they relate to.
- If you run the shop as a sole proprietor, personal tax is separate. The self-employed tax calculator shows $22,126.47 of income tax and CPP on $80,000 of net income in Ontario, though it leaves out EI.
Our sources
GST/HST rates, the $30,000 small supplier limit, the 29 day registration rule and the six year record rule come from the Canada Revenue Agency‘s pages. Example figures come from this site’s calculators, rechecked on 29 September 2026. Prices, features and rankings of accounting products were not verified, and this site doesn’t sell or endorse any of them.
Frequently asked questions
Which accounting software is best for a Shopify store in Canada?
We couldn't verify product rankings or prices. Pick the one that handles your provincial sales tax, refunds and payouts correctly in a trial.
When must a Shopify seller register for GST/HST?
When taxable sales pass $30,000 in a single calendar quarter or over four quarters. You then have 29 days from your effective date.
How much tax do I charge on a $100 sale in Ontario?
13% HST, which is $13.00, for a total of $113.00.
How long should I keep my store records?
Usually six years after the end of the year they relate to.
Does GST/HST apply to online sales inside Canada?
Yes. Goods or services sold online within Canada are subject to GST/HST like any other sale.
All family and benefits calculators
- Self-employed taxes in Canada: income, CPP and GST
How tax works when you are self-employed in Canada: reporting income and expenses, paying both halves of CPP, instalments and when to register for GST