Best e-commerce accounting software in Canada: seven ways to get Shopify, Amazon and Stripe payouts into your books, priced

A2X for Shopify and Amazon sellers with a bookkeeper: from US$29 a month, one journal per payout that matches the deposit with the GST/HST split out, into QuickBooks Online, Xero or NetSuite. Synder from US$65 when Stripe, Square or PayPal deposits are involved. The free Shopify connectors in Xero and QuickBooks Online, or Amaka at $0 to 60 orders, for small Shopify-only stores.

Not at first. The Shopify integration by Xero is free on all Xero plans and the Shopify Connector by QuickBooks is free with a QuickBooks plan; both bring sales, payouts, fees and refunds in. You need A2X or Synder when a bookkeeper takes over, when you add Amazon, Etsy, Stripe or a second store, or when a payout stops matching the deposit and the connector cannot tell you why.

A2X if your money comes through Shopify Payments, Amazon, PayPal, eBay, Etsy or Walmart: it is cheaper from US$29, and its one-journal-per-payout output is the cleanest for a bookkeeper. Synder if you also take Stripe or Square, because A2X does not read them; Synder starts at US$65 for 1,000 synced transactions and can post per transaction. Many Canadian bookkeepers run A2X by default and Synder only where a processor forces it.

In US dollars, excluding Canadian tax. Shopify: Mini US$29 to 200 orders a month, Basic US$45 to 500, Professional US$79 to 2,000, Premium US$115 to 5,000 and up to US$289 at 20,000. Amazon: Mini US$29 to 200, Starter US$59 to 1,000, Standard US$79 to 5,000. Multi-channel: US$89 to 1,000 combined orders, US$115 to 2,000, US$169 to 5,000, US$229 to 10,000. Every plan has a free trial with all features and a 30-minute onboarding session.

No. A2X reads Shopify, Amazon, eBay, Etsy, Walmart and PayPal payouts. Stripe deposits need Synder, which also reads Square and PayPal. A store on Shopify Payments plus Stripe for invoices typically runs A2X for the store and Synder for Stripe, or Synder for both.

They read the tax the platform collected on each order and post it to a tax rate or liability account in your ledger, separate from revenue, so the GST/HST return picks it up. A2X maps tax collected to your ledger tax rates; the QuickBooks connector tracks taxes collected by Shopify; Synder automates sales tax across platforms; Link My Books groups tax rates by product. What no tool decides is whether you should be collecting, or which province’s rate applies; that is in our e-commerce GST/HST guide.

One summary per payout, for almost every Canadian store. A2X, Link My Books, Amaka and the Xero connector post summaries, which keeps a ledger with 2,000 orders a month readable and reconciles to the bank deposit. Synder can post every transaction, which is useful for customer-level records but fills the file fast. Your bookkeeper will have an opinion; ask before choosing.

A2X: it was built on Amazon settlements and handles FBA fees, reserves and reimbursements line by line, from US$29 for 200 orders and US$59 for 1,000. Link My Books is the alternative for sellers on Amazon plus eBay and Etsy who want one subscription across marketplaces. The Xero and QuickBooks Shopify connectors do not read Amazon at all.

A2X publishes a Canadian-readable price table in US dollars and maps tax to Canadian ledger rates; Link My Books prices through a calculator in GBP, USD or AUD and its tax features are written around UK VAT. Link My Books covers more marketplaces on one subscription (Amazon, eBay, Etsy, Shopify, Walmart US, TikTok Shop, WooCommerce, Square). For Shopify and Amazon in Canada we default to A2X; for an eBay and Etsy heavy seller, trial both.

The ones that post one summary per payout matched to the deposit: A2X, Link My Books, Amaka and, at a simpler level, the Xero and QuickBooks Shopify connectors. The payout journal lands in the ledger, the bank feed shows the deposit, and reconciliation is a one-click match instead of a search for why $9,412.18 arrived. Synder reconciles too, per transaction or summarised.

Synder (Stripe, Square, PayPal, Clover and 30+ others) reads gateway deposits directly and posts them to QuickBooks Online or Xero. A2X reads PayPal only; Amaka and Link My Books read Square only. Xero and QuickBooks themselves have separate Stripe and PayPal feeds, but those import transactions rather than reconciling payouts.

Yes, within limits. A2X keeps 3 months of history on Mini, 6 on Basic, 12 on Professional and the maximum available on Premium. Link My Books imports the last 90 days of settlements during its trial. Amaka backsyncs 1 day on Free, 90 days on Premium and 365 on Premium+. Synder offers historical import on supported platforms.

Three: the Shopify integration by Xero (free on all Xero plans), the Shopify Connector by QuickBooks (free with a QuickBooks plan) and Amaka (free to 60 orders a month with one integration; Square to Xero is free without a limit). All three cover a single Shopify or Square store; Amazon and multi-channel selling need a paid tool.

Because the deposit is gross sales minus discounts, minus refunds, plus the tax you collected, minus the processor fee charged on the tax-inclusive amount, minus per-transaction cents, chargebacks and gift card adjustments. The payout decoder on this page shows the journal for one period. A sync tool writes that entry for every payout; posting the deposit as sales understates revenue and fees and never records the tax you owe.