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Accounting for ecommerce and marketplace sellers

Reviewed by EverStone CPA · July 2026

Selling online creates sales tax obligations in provinces you have never visited, and platform reports that do not agree with your bank. What differs, and where to read more.

Quick answer: Ecommerce accounting differs from ordinary retail accounting because sales tax follows the customer’s province rather than yours, marketplaces may collect tax on your behalf while your own filing obligation continues, processor deposits arrive net of fees, and inventory has to be costed to a landed value.

Three-column summary of ecommerce accounting: sales tax follows the customer’s province with provincial sales taxes needing their own registrations and marketplaces sometimes collecting on your behalf, processor payouts settle net so the deposit is not the revenue, and cost of goods sold depends on landing inventory cost correctly
A retailer whose customers are everywhere, paid net of everything.

An online store is a retailer whose customers are everywhere. That single fact turns sales tax from one rate into several, turns a bank deposit into a figure that no longer matches any invoice, and turns inventory into a number that has to be built rather than read off a shelf. None of it is exotic, but almost none of it appears in general small business guidance.

What is different about ecommerce accounting

Sales tax follows the customer, not the seller

Place-of-supply rules mean the rate charged is generally determined by where the goods are delivered. A registered seller in BC shipping to Ontario charges the Ontario rate, and to Alberta a different one again. One registration covers GST/HST across the participating provinces, but the rate applied has to vary order by order — which is a configuration problem in the storefront long before it is an accounting one.

Provincial sales taxes are separate registrations

British Columbia’s PST, and the equivalent taxes in Saskatchewan, Manitoba and Quebec, sit outside the GST/HST system entirely. Selling into those provinces can create a registration obligation with its own thresholds, returns and rules about what is taxable. A seller who assumes one GST/HST number covers the whole country will be wrong in at least four provinces.

Marketplaces may collect the tax, but the obligation stays yours

Under the marketplace facilitator rules, platforms are often required to collect and remit GST/HST on sales made through them. That does not eliminate your own registration or filing responsibilities, and it means marketplace sales and direct-website sales are reported differently on the same return. Reporting platform-collected tax as if you had collected it is a common and awkward error to unwind.

Exports are zero-rated, which changes the whole return

Goods shipped outside Canada are generally zero-rated: no tax charged, input tax credits still recoverable. A seller with substantial US or international volume therefore tends to file for refunds rather than remittances, and the evidence of export — shipping records, customs documents — is what supports the treatment on review.

The deposit is not the revenue

Payment processors and marketplaces settle net: gross sales less commissions, advertising, refunds, chargebacks, shipping labels and reserve. Booking the deposit as revenue understates both sales and expenses, misstates GST, and makes gross margin meaningless. Every payout has to be decomposed back to its components, which is why ecommerce bookkeeping is fundamentally a reconciliation exercise.

Inventory has to be costed, not guessed

Cost of goods sold is the largest number on most ecommerce income statements, and it depends on landing costs correctly: product cost plus freight, duty and any non-recoverable tax. Add multi-currency purchasing, goods in transit at year end and stock held in a fulfilment warehouse, and a physical count at the year-end date stops being a formality.

The guides, tools and pages for this vertical

Sales tax across provinces and borders

Calculators

  • GST/HST calculator — works out the tax on an order at any provincial rate. Useful while setting up storefront tax settings.
  • Quick method versus regular — compares the two filing methods. Rarely the answer for an inventory business, but worth checking.
  • Corporate tax estimator — a first estimate of the year’s corporate tax, useful once margins are known.

Inventory, margin and year end

Service and city pages

Who this fits

This hub is written for incorporated online retailers running their own storefront, marketplace sellers on the large platforms, wholesalers and distributors selling to retailers, subscription-box and direct-to-consumer brands, and dropshippers who never touch the goods. It also fits a bricks-and-mortar retailer adding an online channel, where the new complication is that sales are suddenly leaving the province. Sellers of digital products or services face the same place-of-supply questions with none of the inventory ones.

How this runs remotely

EverStone CPA is a sole-practitioner CPA firm at 32615 South Fraser Way in Abbotsford, BC, working fully remotely — which suits a business that is already entirely digital. Storefront, marketplace and processor reports are exported or connected directly to the ledger, so there is nothing to deliver anywhere. Meetings happen by video, and GST/HST, PST and corporate returns are filed electronically. Because none of the work depends on location, a seller shipping from a Vancouver warehouse and one shipping from Ontario are handled the same way.

About this page
EverStone CPA

Prepared and reviewed by a Chartered Professional Accountant at EverStone CPA, an Abbotsford CPA firm working fully remotely with small businesses and incorporated contractors across the Fraser Valley and Canada. About the firm →  ·  Book a free consult →

Common questions

Ecommerce accounting — common questions

Do I charge my own province’s rate or my customer’s?+
Generally the customer’s. Place-of-supply rules look to where the goods are delivered, so a BC seller shipping to Ontario charges the Ontario rate. One GST/HST registration covers the participating provinces, but the rate has to vary by order, which makes the storefront tax configuration part of the compliance.
Amazon collects the tax on my sales. Do I still have to file?+
Yes. Marketplace facilitator rules can make the platform responsible for collecting and remitting on sales made through it, but your own registration and filing obligations continue, and direct sales from your own site are still yours to collect on. Marketplace and direct sales are reported differently on the same return.
Do I need to register for PST as well as GST?+
Possibly. British Columbia’s PST and the equivalent taxes in Saskatchewan, Manitoba and Quebec sit outside the GST/HST system, with their own registration thresholds and their own rules about what is taxable. Selling into those provinces can create an obligation independent of your GST/HST number.
Why does my bookkeeping never match my platform sales report?+
Because the payout is net. Commissions, advertising, refunds, chargebacks, shipping labels and reserve are all deducted before the deposit lands. Recording the deposit as revenue understates sales and expenses and misstates the tax. Each payout has to be broken back into its components for the ledger to be right.
How should inventory be valued at year end?+
At landed cost — the product cost plus freight, duty and any non-recoverable tax to get it to you — using a consistent method year over year. Goods in transit and stock held at a fulfilment centre still belong to you and still have to be counted. Cost of goods sold is only as accurate as that number.
Do I charge tax on orders shipped to the United States?+
Goods exported from Canada are generally zero-rated, so no GST/HST is charged while input tax credits on your costs remain recoverable. The shipping and customs records are what support the treatment if the return is reviewed, so they need to be kept rather than discarded with the packing slip.

A CPA who has reconciled a marketplace payout

Multi-province sales tax, a marketplace collecting on your behalf, or inventory that never quite ties out — describe how you sell and you will get a straight answer.