# Shopify Bookkeeping Canada: How to Keep Your E-Commerce Books Clean
Why Shopify Bookkeeping Is Different in Canada
- ●Shopify deposits net payouts (after fees) — you must reconcile gross sales, fees, refunds separately
- ●HST/GST on Canadian customer sales must be tracked and remitted
- ●Multi-currency if selling to US customers (USD/CAD exchange)
- ●Inventory COGS must be tracked for accurate profit reporting
- ●Marketplace facilitator rules: Shopify collects HST on your behalf in some provinces since 2021
Shopify Payout Reconciliation: How It Works
Shopify pays you net amounts that include: gross sales minus Shopify fees minus refunds minus chargebacks. Your bookkeeper must record all components separately:
- ●Gross sales — Revenue
- ●Shopify transaction fees — Expense
- ●Shopify subscription — Expense
- ●Refunds — Revenue reversal
- ●Chargebacks — Separate tracking
Step-by-step reconciliation:
1. Download monthly Shopify payout report 2. Import to accounting software via A2X (recommended) or manually 3. Reconcile net deposit against bank statement 4. Verify HST collected matches HST liability account
Recommended: A2X app to automate Shopify to QuickBooks/Xero sync.
HST/GST on Shopify Sales in Canada
- ●If your Shopify store sells to Canadian customers and you're HST-registered: collect and remit HST
- ●Shopify can automatically calculate and collect the correct provincial rate per customer location
- ●You still file the HST return and remit to CRA — Shopify just helps collect it
- ●HST registration required once you exceed $30K/year in Canadian taxable revenue
- ●Zero-rated exports: sales to US/international customers — no HST charged, but ITCs still claimable
Inventory Bookkeeping for Canadian Shopify Sellers
- ●Track COGS (Cost of Goods Sold) for accurate profit reporting
- ●Inventory methods: FIFO, weighted average cost (most common for Shopify sellers)
- ●Year-end inventory count required for T2 corporate returns
- ●Landed cost: include shipping, customs duties, and HST in inventory cost
Best Software for Shopify Bookkeeping in Canada
| Tool | Use | Cost |
|---|---|---|
| A2X | Shopify to QuickBooks/Xero sync | $19–$79/month |
| QuickBooks Online | Accounting | $28–$80/month |
| Xero | Accounting | $20–$60/month |
| Shopify Tax | HST collection | Included |
Should Shopify Sellers Outsource Bookkeeping?
Yes — especially once revenue exceeds $100K/year. Shopify bookkeeping complexity (payouts, multi-currency, inventory, HST) makes DIY risky. A bookkeeper at $500/month saves 10–15 hours/month and ensures CRA compliance.
Frequently Asked Questions
Need professional bookkeeping?
Outsource Bookkeeping delivers CPA-ready financial reports by the 10th of every month — flat rate, no surprises.