Shopify gives you a clean dashboard of orders, payouts, and fees — but it is not a bookkeeping system. Once you reconcile payouts, track COGS, handle sales-tax filings across states, or manage multi-currency revenue, you need a proper accounting platform that talks back to Shopify automatically. We evaluated the top contenders on Shopify integration depth, multi-currency capability, automation of payouts and fees, and whether they scale with a growing store. Here are the things actually worth buying.
QuickBooks Online — Best Overall
QuickBooks Online is the default for good reason. Its native Shopify integration syncs orders, payouts, fees, and refunds automatically — no middleware required.1 Every sale lands in your books as a summary entry, and the platform categorises Shopify transaction fees, shipping costs, and tax collected without manual intervention.
For US-based sellers, QuickBooks handles sales-tax tracking across states and integrates with Avalara for automated filing.2 The reporting suite — P&L, balance sheet, cash flow — is robust enough that your CPA will thank you. The main trade-off: the interface can feel dense, and the mid-tier plans climb quickly as you add users.
Who it's for: Growing Shopify stores that want a set-and-forget accounting backbone with serious tax and reporting muscle.
Xero — Best for International / Multi-Currency
If you sell across borders, Xero is the play. Its multi-currency support is best-in-class: you can invoice, reconcile, and report in over 160 currencies, and it automatically updates exchange rates daily.1 The Shopify integration captures order data, fees, and payouts, and Xero's bank-feed matching makes reconciliation fast.
Xero also shines on VAT/GST handling for EU, UK, and Australian sellers — a headache QuickBooks handles less elegantly outside North America.3 The interface is cleaner and more modern than QuickBooks, though its inventory tracking is lighter, which matters if you manage SKUs inside your accounting tool.
Who it's for: International Shopify sellers — or those planning to expand globally — who need strong multi-currency and VAT support.
Zoho Books — Best All-in-One Ecosystem
Zoho Books is the affordable dark horse. It integrates directly with Shopify to sync orders, products, and payments, and it ties into the broader Zoho ecosystem (CRM, Inventory, Analytics) at a fraction of the cost of the big two.1 For a bootstrapping brand that wants one login for everything — customer management, inventory tracking, and accounting — it's hard to beat.
The automation rules are surprisingly powerful: you can set up workflows that tag transactions, send payment reminders, and update inventory counts without touching a thing. The catch: Zoho's support is thinner, and the interface, while functional, lacks the polish of Xero or FreshBooks.
Who it's for: Cost-conscious Shopify sellers who want an integrated CRM + inventory + accounting stack without paying for separate tools.
FreshBooks — Best for Product + Service Hybrids
Many Shopify sellers also offer setup fees, customisation services, or ongoing support retainers. FreshBooks was built for service businesses, and its Shopify integration handles both product sales and service billing in one place.2 Time tracking, project-based invoicing, and expense categorisation are first-class features.
The Shopify sync brings in order data and fees, and FreshBooks' bank reconciliation is intuitive — less clicking than QuickBooks. Its reporting is less granular for inventory-heavy stores, but for a hybrid model (sell a widget, charge to install it), it's the most natural fit.3
Who it's for: Shopify merchants who sell physical products and bill for services — think custom goods, installations, or subscription support.
How We Chose
Every pick above was evaluated on three axes: Shopify integration depth (does it auto-sync payouts, fees, refunds, and taxes?), multi-currency support (can it handle cross-border sales without manual workarounds?), and pricing scalability (does the cost make sense from $10K to $1M in revenue?).1 All four platforms automate the heavy lifting of e-commerce bookkeeping — the right choice depends on where your store operates and how you sell.
Recomate earns affiliate commissions when you purchase through the links above. We only recommend software we've evaluated against our criteria.
