Do Shopify Fees Have GST? What Canadian Sellers Can Claim Back (2026)

Yes, most fees Shopify bills a Canadian store carry GST or HST. Shopify adds tax to your subscription and most other platform charges based on the province in your billing address, and if you’re registered for GST/HST you can claim that tax back as an input tax credit. If you’re not registered, the tax is simply part of what the platform costs you.

The catch is that one big fee category works differently, and mixing them up creates errors in both directions.

Which Shopify fees carry GST or HST

Shopify’s own billing documentation confirms that Canadian stores are charged applicable taxes on their subscription, and the same treatment applies across most charges on a Shopify invoice: plan fees, app charges billed through Shopify, themes, domains, shipping labels, and the extra transaction fee you pay when you use an outside payment provider instead of Shopify Payments.

The rate follows your billing address. An Ontario store pays 13% HST on its plan, an Alberta store pays 5% GST, and a Quebec store sees QST as well. Provincial taxes are spreading too: effective January 1, 2026, Manitoba applies its 7% retail sales tax to cloud computing services, so Shopify now adds Manitoba RST as a separate line for stores billed to a Manitoba address. Our GST vs HST guide for Shopify sellers breaks down the rates by province.

A $500 monthly Shopify bill in Ontario carries about $65 of HST. Over a year that’s roughly $780, and it’s either recoverable or lost depending entirely on whether you’ve registered.

The exception: Shopify Payments processing fees

The card processing fee Shopify Payments takes from each order, the familiar 2.9% plus 30 cents on a basic plan, is payment processing. Card processing is built mostly on financial services that Canada treats as GST/HST exempt, so Shopify Payments generally doesn’t add GST or HST to those per-order fees. It isn’t a blanket rule, which is exactly why the billing documents matter.

Here’s the trap. Sellers assume every Shopify fee includes tax, back out 13% from their processing fees, and claim input tax credits on tax that was never charged. CRA can deny those credits in a review and add interest on top. The reverse error costs money too: assuming no Shopify fee has tax and leaving real, recoverable GST sitting on the table.

Don’t guess in either direction.

Shopify issues monthly billing documents that show exactly which charges carried tax and how much. Those documents are what supports your claim if CRA ever asks, so keep them.

What registration changes

If your store is registered for GST/HST, the tax on your Shopify fees stops being a cost. You recover it through input tax credits, which means the real price of the platform is the pre-tax amount. If you’re not registered, there’s nothing to claim, and the tax is simply part of the expense. Where the registration line sits, and when crossing it stops being optional, is covered in our guide on whether your Shopify store needs a GST number.

One thing a GST number won’t do is make the tax on your fees disappear. Shopify only removes tax from billing for genuinely exempt organizations, such as registered non-profits and government bodies, and only after a verification process through its support team. A regular corporation with a GST number keeps paying tax on its fees. The number’s job is to let you claim it back.

The bookkeeping trap that loses the claim

Shopify makes this harder than it should be, because fees hit you in two different ways. Your subscription and app charges are billed to your card. Shopify Payments processing fees never arrive as a bill at all; they’re deducted before each payout lands in your bank account.

Stores that record the net deposit as revenue understate their sales and quietly throw away the fee deduction and the tax claim at the same time. We see it constantly on self-prepared Shopify files.

All Shopify fees are legitimate business deductions either way. If you claim the ITC, the deductible expense is the pre-tax fee. If you’re not registered, the whole amount including the tax is your cost. Getting that split wrong means either double counting the tax or losing it entirely.

Frequently asked questions

Are Shopify fees tax deductible in Canada?

Yes. Subscription fees, app charges, transaction fees, and payment processing fees are all deductible business expenses. If you’re registered for GST/HST and claim input tax credits, you deduct the pre-tax amount on fees that carried tax; if you’re not registered, you deduct the full amount including the tax.

Does Shopify charge GST on subscription fees in Canada?

Yes. Shopify charges GST, HST, or QST on subscriptions for Canadian stores based on the billing address, and from January 1, 2026 it also charges 7% Manitoba RST for stores billed to a Manitoba address.

Is there GST on Shopify Payments processing fees?

Generally no. Card processing is built mostly on financial services that Canada treats as GST/HST exempt, so Shopify Payments generally doesn’t add GST or HST to those per-order fees. Claiming input tax credits on them anyway is a common error that CRA can reverse with interest. Confirm against Shopify’s monthly billing documents rather than assuming.

Can I stop Shopify from charging tax on my fees by giving them my GST number?

No. Tax exemption on Shopify billing is limited to qualifying organizations like registered non-profits and government entities, and it has to be approved through Shopify support. A standard business keeps paying the tax and recovers it through input tax credits instead.

Related guides

• Shopify GST/HST for Canadian sellers: the full decision tree
• GST vs HST for Shopify sellers: rates by province
• Do you need a GST number for Shopify in Canada?
• Shopify Tax vs Basic Tax: what the fee buys Canadian stores
• Our GST/HST registration and filing service

Not sure what you can claim back?

We prepare GST/HST returns for Shopify sellers across Canada, including the cleanup when fee taxes have been missed or overclaimed for years. Contact us and we’ll tell you where you stand.