Selling on Shopify, Amazon FBA, WooCommerce, and Etsy creates financial complexity that standard desktop accounting software cannot solve out of the box. Between gross sales, platform processing fees, refunds, and provincial sales taxes, store owners often find their books in disarray.
The Payout Reconciliation Trap
When Shopify or Amazon deposits $8,450 into your corporate bank account, that is not your revenue. That deposit is a net payout: gross sales minus referral fees, FBA pick-and-pack charges, shipping labels, and customer refunds. Recording only the bank deposit will severely distort your income statements and lead to massive GST/HST filing discrepancies.
| Platform / Channel | Common Withholdings & Fees | Proper Accounting Treatment |
|---|---|---|
| Shopify Payments | Credit card processing (2.9% + 30¢), transaction fees, chargebacks | Reconcile gross order total to Stripe/Shopify clearing account; record fees as expense. |
| Amazon FBA | Referral fee (15%), FBA fulfillment, storage fees, advertising fees | Parse bi-weekly settlement reports into gross sales, fees, and inventory reimbursements. |
| Etsy | Listing fees, payment processing, regulatory operating fee | Sync monthly payment account statements with sales ledger. |
“Accurate e-commerce bookkeeping requires automated settlement clearing accounts. You must account for gross sales and expenses separately—not just lump bank deposits as revenue.”
— InstaAccountant E-Commerce Practice Lead
Canadian Sales Tax (GST/HST & PST) by Province
Under Canadian Place of Supply rules, sales tax is charged based on the destination of the customer, not the seller’s province:
- Ontario: 13% HST
- British Columbia: 5% GST + 7% PST (separate provincial registration required)
- Quebec: 5% GST + 9.975% QST (under Quebec e-commerce regime)
- Alberta: 5% GST only (no provincial sales tax)
InstaAccountant connects directly to your Shopify and Amazon seller central accounts to provide seamless monthly reconciliations and automated tax filings.
