Shopify, Amazon, and Etsy each pay out differently, tax differently, and take their cut differently — which means treating them as one interchangeable "online sales" bucket in your books hides more than it reveals.

Your Payout Isn't Your Revenue

Platform payouts arrive net of platform fees, payment processing fees, and sometimes advertising spend, all bundled into one deposit. Record the full sale amount as revenue and each fee type as its own expense — not just the net number that hits your bank account. Skipping this understates both your sales and your actual costs.

Marketplace Facilitator Rules Change Who Collects GST/HST

For sales made through certain marketplaces, the platform itself may be required to collect and remit GST/HST on your behalf, rather than you handling it directly — and this can work differently depending on whether you're selling through your own Shopify store or through a marketplace like Amazon or Etsy. Know which of your sales channels are handling this for you and which require you to charge and remit it yourself.

One thing that catches people even after they've sorted out who's collecting: those marketplace-facilitated sales still need to show up on your own GST/HST return, even when the platform already remitted the tax to the CRA. Leaving them off because "the platform already dealt with it" creates a mismatch between what the marketplace reports and what your return shows — and that mismatch is exactly the kind of thing that draws a follow-up letter.

Assuming one channel works like another is a common and costly mistake.

Inventory and Cost of Goods Sold

Track what you paid for inventory separately from what you sell it for. Cost of Goods Sold should reflect the actual cost of the specific items sold in a period, not just total purchases — which means tracking inventory levels, not recording every purchase as an immediate expense.

Multiple Sales Channels Need Separate Visibility

If you sell across Shopify, Amazon, and Etsy at once, each channel has different fee structures and different tax handling. Track revenue and fees by channel, at least at a summary level, so you can see which channels are actually profitable once fees are accounted for — not just which ones move the most volume.

What You Can Deduct

• Cost of goods sold (inventory)
• Platform and payment processing fees
• Advertising and marketing spend
• Shipping and packaging costs
• Software and apps used to run your store
• Warehousing or fulfillment service fees

FAQ

Do I need separate bookkeeping for each sales channel? Not fully separate books, but separate tracking within your books — by class or location in QBO (Plus plan and up) or a similar tag if you're on a different tier — so you can see channel-level profitability instead of one blended number.

How do I handle inventory I use for samples or giveaways? Remove it from inventory and record it as a marketing or promotional expense at cost, rather than leaving it sitting in inventory or ignoring it entirely.

Does it matter if my inventory is stored in a fulfillment warehouse instead of at home? Not for the bookkeeping treatment of the inventory itself, but the fulfillment fees themselves are a deductible operating expense, separate from the cost of the inventory.

Platform fees, marketplace GST/HST rules, inventory tracking — Margot knows the layers that make e-commerce bookkeeping different from a regular retail business. Ask Margot a question right now.