Shopify + QuickBooks Online Integration
QuickBooks connections expire. Duplicate transactions appear. Processor fees get recorded wrong. We build integrations that fix these problems before they cost you hours of reconciliation.
Integration goals
Revenue recognition, tax sync, and multi-currency support for Shopify merchants who need their books to stay clean.
- Revenue recognition that matches actual deposits (net of fees)
- Tax liabilities tracked correctly across jurisdictions
- Multi-currency transactions recorded at correct exchange rates
- Automated reconciliation between Shopify payouts and QuickBooks deposits
- No duplicate transactions from payment gateway double-sync
What breaks in practice
We've seen these patterns destroy integrations. Here's what to watch for:
Connection expires every 6 months
OAuth tokens need manual reauth. Sync stops. No one notices until month-end close reveals missing revenue.
Duplicate transactions from payment gateway sync
Both Shopify and Stripe/PayPal sync to QuickBooks. Same transaction appears twice. Your revenue is overstated by 30%.
Fees not mapped correctly → inflated revenue
Shopify deposits net of processing fees. If integration records gross revenue, your books are wrong and so is your tax liability.
Tax codes mismatch between systems
Shopify's flexible tax engine doesn't align with QuickBooks tax items. Journal entries have wrong tax accounts. Compliance risk.
Multi-currency conversions at wrong rates
CAD sale recorded at yesterday's exchange rate. Month-end reconciliation reveals $10K variance.
How we build it
Daily batch sync with detailed transaction mapping. Shopify payouts are reconciled against individual orders to ensure revenue, fees, and taxes are recorded correctly.
Technical details
- QuickBooks Online API v3 (REST + OAuth 2.0)
- Shopify Admin API for order and payout data
- Payout-based revenue recognition (not order-based)
- Fee mapping: Shopify fees, payment processor fees, transaction fees all tracked separately
- Tax sync with custom mapping from Shopify tax lines to QuickBooks tax items
- Multi-currency: record transactions in customer currency + base currency
Sync strategy
Daily batch sync aligned with Shopify payout schedule. Historical backfill for initial setup. Reconciliation runs weekly.
Conflict resolution
Shopify is source of truth for revenue and orders. QuickBooks is source of truth for chart of accounts. Discrepancies trigger manual review.
Phased approach
We break complex integrations into manageable phases with clear milestones.
Discovery & Mapping
1 week- Audit QuickBooks chart of accounts
- Map Shopify revenue types to QuickBooks income accounts
- Define fee accounts (Shopify, Stripe, PayPal, etc.)
- Map tax jurisdictions to QuickBooks tax items
- Decide on revenue recognition method (payout vs. accrual)
Core Sync (Revenue & Fees)
2 weeks- Build payout sync from Shopify to QuickBooks deposits
- Map individual transactions within each payout
- Implement fee breakout (payment processing, Shopify fees)
- Add tax mapping with fallback for unmapped jurisdictions
- Handle refunds and chargebacks
Multi-Currency & Edge Cases
1 week- Implement multi-currency support with daily rates
- Handle partial refunds and gift card redemptions
- Map discounts and promotional codes
- Build reconciliation report (Shopify payouts vs. QuickBooks deposits)
Testing & Launch
1 week- Historical data backfill (last 90 days)
- UAT with finance team
- Set up monitoring for auth token expiration
- Deploy alerting for sync failures and reconciliation variances
- Go live with weekly reconciliation reviews
Requirements checklist
To build this integration, we'll need access to the following:
Book a QuickBooks integration consult
Let's discuss your QuickBooks Online integration requirements. We'll walk through your current setup, pain points, and build a custom implementation plan.