GST/HST for Shopify and Amazon Sellers in Canada: Registration, Rates and Marketplace Rules
Selling on Shopify or Amazon from Canada? Learn when the $30,000 GST/HST registration threshold hits, which rate to charge each province, when Amazon collects tax for you, and how to claim input tax credits on your fees.
If you sell on Shopify or Amazon from Canada, you must register for GST/HST once your worldwide taxable sales pass $30,000 in a single calendar quarter or over four consecutive quarters. The rate you charge depends on the province you ship to, from 5% in Alberta to 15% in New Brunswick, Newfoundland and Labrador, and Prince Edward Island. Amazon collects tax on some sales under marketplace rules, but Shopify collects nothing unless you configure it, and neither platform files a GST/HST return for you.
When do Shopify and Amazon sellers have to register for GST/HST?
The CRA treats you as a small supplier while your worldwide taxable sales stay at $30,000 or less across the last four consecutive calendar quarters. Cross that line and registration stops being optional. The CRA's registration rules set two triggers, and the timing is different for each:
- You exceed $30,000 in one calendar quarter. You lose small-supplier status immediately. Your effective registration date is no later than the day of the sale that pushed you over, and GST/HST applies to that very sale. A Shopify store that does $34,000 in Q4 alone owes tax on the order that crossed the line.
- You exceed $30,000 over four consecutive quarters. You keep small-supplier status for one more month after the quarter in which you crossed the threshold, then you must charge GST/HST starting with your first sale after that grace month.
Either way, you have 29 days from your effective date to actually register. Note the test is worldwide taxable supplies, not profit and not Canadian sales only, so US-marketplace revenue counts too. Many sellers register voluntarily before hitting $30,000 because registration unlocks input tax credits on inventory, fees and software from day one. We unpack the common misconceptions in Tax Myth vs Fact: Do You Need to Register for GST/HST in Canada?
What GST/HST rate do you charge on each order?
For physical goods, the place-of-supply rule is simple: charge the rate of the province where the goods are delivered. A $100 order shipped to Toronto carries $13 of HST. The same order shipped to Calgary carries $5 of GST. Shipped to Halifax, it carries $14, because Nova Scotia cut its HST from 15% to 14% on April 1, 2025. Here are the current rates, which you can confirm on the CRA's rate page:
| Province / Territory | GST or HST | Provincial sales tax | Combined rate |
|---|---|---|---|
| Alberta, Yukon, NWT, Nunavut | 5% GST | None | 5% |
| British Columbia | 5% GST | 7% PST | 12% |
| Saskatchewan | 5% GST | 6% PST | 11% |
| Manitoba | 5% GST | 7% RST | 12% |
| Ontario | 13% HST | Included in HST | 13% |
| Quebec | 5% GST | 9.975% QST | 14.975% |
| Nova Scotia | 14% HST (since April 1, 2025) | Included in HST | 14% |
| New Brunswick, Newfoundland and Labrador, PEI | 15% HST | Included in HST | 15% |
Your GST/HST registration covers the GST and HST columns only. PST in British Columbia and Saskatchewan, RST in Manitoba and QST in Quebec are separate provincial systems with their own registration rules and thresholds, so check each province's requirements once you ship meaningful volume there.
When does Amazon collect GST/HST for you, and when is it your job?
Since July 1, 2021, Canada's digital economy rules make marketplace operators like Amazon the "deemed supplier" on certain sales. Whether Amazon or you handles the tax depends on your registration status.
If you are not registered for GST/HST
Amazon is required to collect and remit GST/HST on sales it facilitates for non-registered vendors when the goods ship from within Canada, which includes inventory sitting in Canadian FBA warehouses. The tax happens in the background and never touches your payout. This catches many small FBA sellers off guard in the other direction: they assume they owe tax they actually don't, or they assume Amazon's collection covers their Shopify store too. It does not.
If you are registered
Once you register and enter your GST/HST number in Seller Central, the responsibility shifts back to you. Amazon calculates the tax and passes it through in your disbursements, but you are the one who must report and remit it to the CRA. Registering and forgetting to update Seller Central, or updating Seller Central and forgetting to file, are two of the most common e-commerce compliance failures we see.
What about PST, RST and QST on marketplace sales?
British Columbia (from July 1, 2022), Manitoba (from December 1, 2021), Saskatchewan and Quebec all have their own marketplace rules that generally put the provincial tax on the platform for sales it facilitates. In practice, Amazon typically collects and remits those provincial taxes on marketplace orders itself, regardless of your GST/HST status. Your own website sales are a different story, which brings us to Shopify.
Does Shopify collect and remit GST/HST for you?
No. Shopify is not a marketplace under Canadian tax law, so the deemed-supplier rules never apply to your own store. Shopify will calculate and charge tax at checkout only after you enter your registration numbers in your tax settings, the collected tax lands in your payouts mixed with everything else, and Shopify does not file or remit anything to the CRA or the provinces on your behalf. Skip the setup and you are quietly absorbing the tax out of your margin, because the CRA still assesses the GST/HST you should have collected on those sales. On a $200,000 revenue year in Ontario, that is roughly $26,000 of HST coming out of your own pocket. If you sell direct to customers in BC, Saskatchewan, Manitoba or Quebec, you may also need separate provincial registrations once you pass each province's threshold. Our e-commerce accounting service handles this multi-channel, multi-tax setup as standard.
What input tax credits can online sellers claim?
Registration is not just an obligation, it is a refund mechanism. As a registrant you recover the GST/HST you pay on business inputs through input tax credits (ITCs), including:
- Amazon referral and FBA fees, where GST/HST is charged on your fee invoices
- Shopify subscription and app charges that include Canadian sales tax
- Inventory and packaging purchased from Canadian suppliers
- Courier and freight charges, software subscriptions and accounting fees
- GST paid at the border on commercial imports where you are the importer of record
The numbers are material. A seller doing $200,000 on Amazon.ca typically pays $30,000 or more in Amazon fees; at 13% HST that is around $3,900 of recoverable tax in a single year. Keep every fee invoice and customs form, because the CRA requires you to hold supporting records for six years.
How do you reconcile Amazon and Shopify payouts for your GST/HST return?
The biggest filing errors come from working off bank deposits. An Amazon payout is net of fees, refunds, reserves and advertising, and it blends tax Amazon remitted itself with tax it passed to you. Book the deposit as revenue and you will understate sales, misreport tax collected and miss ITCs all at once. The fix is reconciling from settlement data: tools like A2X split each payout into gross sales, refunds, fees and tax collected by province, and separate what Amazon remitted as deemed supplier from what you must remit. We cover the toolstack in Pick the Right Tools, Don't Do It Manually.
Filing frequency depends on size: $1.5 million or less in annual taxable sales defaults to annual filing (you can elect quarterly or monthly), between $1.5 million and $6 million defaults to quarterly, and above $6 million is monthly. For reporting periods beginning on or after January 1, 2024, GST/HST returns must be filed electronically. Our fixed monthly pricing includes this reconciliation and filing work, so a growing seller is not billed by the hour for it.
Frequently Asked Questions
Do I need to register for GST/HST if I only sell on Amazon FBA?
Not automatically. While you stay under the small-supplier threshold and unregistered, Amazon collects and remits GST/HST on your Canadian FBA sales as the deemed supplier. But once your worldwide taxable sales pass $30,000, or you want to recover the GST/HST built into your Amazon fees and inventory costs, you need your own registration. After registering, enter your number in Seller Central immediately, because from that point the GST/HST flows to you and you must remit it.
Do my Amazon sales count toward the $30,000 threshold?
The small-supplier test looks at your worldwide taxable supplies, so as a starting point count everything: Amazon.ca, Amazon.com, Shopify, Etsy, eBay and wholesale. The deemed-supplier rules add technical wrinkles for unregistered sellers about which sales are attributed to the platform, so do not assume you are under the line based on one channel. Track gross sales across all channels monthly and get advice before you drift past the threshold, because backdated registration comes with interest.
Does Shopify charge GST/HST automatically?
Only after you set it up. Shopify calculates tax at checkout based on the registration numbers and regions you enter in your tax settings; with no setup, orders go out tax-free even when you are legally required to charge. Shopify also never remits to the CRA or files returns, whatever it collects simply arrives inside your payouts. You or your accountant must track tax collected by province, prepare the return and send the money in by the deadline.
Can I claim GST/HST back on my Amazon seller fees?
Yes, if you are registered and GST/HST was charged on the fees. Check your monthly Amazon fee invoices: where tax appears on referral fees, FBA fulfillment fees and advertising, those amounts are input tax credits that directly reduce your remittance. A seller paying $2,500 a month in fees with 13% HST on top is leaving roughly $325 a month on the table by not claiming, nearly $4,000 a year. Keep the invoices, since the CRA can ask for them for six years.
What happens if I passed $30,000 months ago and never registered?
The CRA will register you retroactively to the date you crossed the threshold, and you owe the GST/HST you should have collected from that date, plus interest, even though you never charged it to customers. On $80,000 of unregistered Ontario sales that is roughly $10,400 out of pocket before interest. The upside is that you can usually claim ITCs for the same period to soften the hit. Act before the CRA contacts you; voluntary correction is always the cheaper path.
Not sure whether you have crossed the threshold, or tired of untangling Amazon settlements at filing time? Book a free 30-minute consultation with SNF Accounting. We work with Shopify and Amazon sellers across Canada on fixed pricing from $199 per month, so registration, reconciliation and every GST/HST filing are handled without hourly surprises.
