How to Handle Bookkeeping Across Shopify and Amazon for a Canadian Store
Canadian store owners selling on both Shopify and Amazon must book each platform as a separate revenue stream, reconcile payouts (not gross sales) to their bank, and apply the correct GST/HST rules for each channel — because the two platforms report money completely differently and mixing them up silently destroys your books.
How to Handle Bookkeeping Across Shopify and Amazon for a Canadian Store
Canadian store owners selling on both Shopify and Amazon must book each platform as a separate revenue stream, reconcile payouts (not gross sales) to their bank, and apply the correct GST/HST rules for each channel — because the two platforms report money completely differently, and mixing them up silently destroys your books.
Why This Is Harder Than It Looks
Shopify and Amazon both land money in your bank account, but they arrive differently, mean different things, and carry different tax implications. Treating them the same way is one of the most common — and costly — bookkeeping mistakes Canadian hybrid sellers make.
- Shopify pays out close to what the customer paid, minus payment processing fees. Your Shopify reports reflect gross sales and GST/HST collected.
- Amazon pays out a net figure after deducting referral fees, FBA fulfillment fees, storage fees, advertising charges, and any other Amazon-side adjustments. The settlement report is dense and not self-explanatory.
If you simply deposit both payouts and call them "sales," you are understating your expenses and overstating your margins — every single month.
The Core Rule: Reconcile to the Settlement Report, Not the Deposit
Your bank deposit from Amazon is not your revenue. It's your revenue minus a pile of Amazon fees. Here's the correct approach:
- Record gross Amazon sales as revenue (what customers actually paid).
- Record Amazon fees line by line as expenses (referral fees, FBA fees, storage, ads).
- Reconcile the net to what hit your bank account.
On the Shopify side, your payout is close to gross — but Shopify Payments fees still need to be separated out as a payment processing expense, not netted against revenue.
GST/HST: Each Platform Has Its Own Rules
This is where Canadian sellers get tripped up most.
- Shopify (your own storefront): You are the seller of record. You collect GST/HST from Canadian customers, hold it, and remit it to the CRA. This amount must be tracked separately — it is never your income.
- Amazon Canada (third-party marketplace): Under Canada's digital services tax rules, Amazon is required to collect and remit GST/HST on sales made through its marketplace on your behalf. You generally do not collect it again — but your bookkeeping must reflect this so you don't accidentally double-count tax owing.
Getting this wrong doesn't just create messy books — it creates a GST/HST remittance error that shows up at audit time.
Practical Setup: How to Structure Your Books
- Separate revenue accounts for Shopify sales and Amazon sales. Never blend them into one "e-commerce revenue" line.
- Separate expense accounts for Shopify fees, Amazon referral fees, FBA fees, and Amazon advertising. Each has different margin implications.
- A clearing account (sometimes called a "merchant reserve" account) for Amazon settlements, so you can post the gross amounts and fees before the net clears to your operating account.
- Monthly reconciliation of each platform's payout report to your bank statement — not quarterly, monthly. Discrepancies compound fast.
What This Tells You About Your Business
Done right, this structure shows you something most hybrid sellers never see clearly: which channel is actually more profitable after fees. Amazon often looks bigger on the top line but quietly bleeds margin through fees. Shopify often has better margins but higher customer acquisition costs. You can't make smart growth decisions without knowing this split.
This is exactly the kind of multi-platform financial picture that a fractional CFO lens — like the work SGML Accounting does with Canadian hybrid sellers — is built to surface. The bookkeeping isn't just compliance; it's the intelligence layer for your business.
Quick Reference: Shopify vs. Amazon Bookkeeping
| Shopify | Amazon | |
|---|---|---|
| Revenue to record | Gross sales | Gross sales (not the deposit) |
| Key expenses | Payment processing fees | Referral, FBA, storage, ads |
| GST/HST collected by | You | Amazon (marketplace facilitator) |
| Payout timing | Daily or weekly | Bi-weekly settlements |
| Reconciliation doc | Shopify Payments payout report | Amazon Settlement Report |
Frequently asked questions
Do I need two separate QuickBooks or Xero accounts for Shopify and Amazon?
No — one accounting file is correct. You separate them using different revenue and expense accounts (or classes) within the same file, so you can see each channel's performance without fragmenting your overall financials.
Does Amazon remit GST/HST on my behalf for Canadian sales?
Yes. Amazon is designated as a marketplace facilitator under Canadian GST/HST rules and is required to collect and remit GST/HST on third-party sales made through Amazon.ca. You should not collect or remit GST/HST on those same sales yourself — but confirm with your accountant how this interacts with your overall GST/HST registration.
Why does my Amazon deposit never match my Amazon sales report?
Because Amazon deducts referral fees, FBA fulfillment and storage fees, advertising costs, and any reserves before sending your settlement. Your deposit is the net after all of that. You need to book the gross sales and the fees separately — the deposit is just the end result.
How often should I reconcile my Shopify and Amazon accounts?
Monthly, at minimum. Amazon settles bi-weekly and Shopify pays out frequently, so monthly reconciliation catches discrepancies before they compound. Waiting until tax season to sort this out typically means hours of painful cleanup — and sometimes missed deductions.
Can I use an app to automate this, or do I need an accountant?
Apps like A2X can automate the mapping of Amazon and Shopify settlements into Xero or QuickBooks, which helps significantly. But automation maps transactions — it doesn't catch GST/HST errors, misclassified fees, or margin problems. A knowledgeable accountant (ideally one familiar with Canadian multi-platform e-commerce) adds the judgment layer the apps can't.
Every business's platform mix, registration status, and tax obligations are different — the specifics of your GST/HST setup and bookkeeping structure are worth reviewing with a qualified Canadian accountant.