Running a Shopify store is already a full-time job you don’t need the added stress of manual bookkeeping, reconciling payout mismatches, or tax errors at quarter-end.
This super-helpful FAQ guide answers your top 20 most asked questions about integrating Shopify with Xero or QuickBooks, so you can save time, reduce errors, and focus on growing your business.
How to Connect Shopify to Xero or QuickBooks
1. How do I connect Shopify to Xero?
You’ll need a third-party integration tool like A2X, Amaka, or Snyder. These apps pull Shopify sales, fees, and payouts straight into Xero, turning a bookkeeping nightmare into a clean, automated system.
2. How do I connect Shopify to QuickBooks?
Apps like QuickBooks Connector (OneSaas), A2X, or Bold Commerce handle this. They let you sync Shopify sales, taxes, and payment gateway data directly into your chart of accounts.
3. Can I connect Shopify to Xero or QuickBooks without using an app?
Technically, yes with manual CSV exports. But we strongly advise against it. Manual imports increase the risk of errors, duplicates, and reconciliation issues. Plus, it’s not scalable as your business grows.
How Often Does It Sync?
4. How often will data sync between Shopify and Xero/QuickBooks?
Most apps offer daily automatic syncs, with options to sync hourly, manually, or in real time (depending on your plan).
5. Can I choose what gets synced?
Absolutely. You can customise which data points sync such as orders, fees, refunds, shipping, or payment gateways and where each one lands in your accounting software.
6. Will it sync historical data from Shopify?
Yes many apps offer backdating or historical imports (sometimes for an additional fee). Perfect if you’re migrating or catching up your books.
What About Multi-Currency?
7. Does the integration support multiple currencies?
Yes if your Xero or QuickBooks plan includes multi-currency, and your chosen integration app supports it. A2X, for example, handles multi-currency extremely well.
8. How are exchange rates handled?
Most apps pull the Shopify exchange rate or use the accounting platform’s FX rate. This can affect how foreign currency sales appear in reports.
How to Fix Errors and Common Issues
9. Why don’t my Shopify payouts match in Xero or QuickBooks?
The usual culprit? Shopify fees, refunds, or timing issues. Tools like A2X create payout summaries that match Shopify deposits exactly, making reconciliation effortless.
10. What should I do if transactions don’t sync?
Check your integration app’s error logs. Common issues include missing account mappings, deleted SKUs, or expired API connections.
11. How do I prevent duplicate or missing entries?
Most apps let you set rules for reprocessing or skipping entries. Always review sync settings and avoid double entries through manual uploads or multiple apps.
Product, Tax & Inventory Questions
12. Will my product SKUs sync from Shopify to Xero/QuickBooks?
Not usually. Most integrations handle financial data, not product listings. For inventory control, use an inventory management app alongside your accounting integration.
13. How does it handle VAT or GST?
You can map Shopify tax rates to the correct VAT/GST codes in Xero or QuickBooks. This is vital for accurate returns and audits.
14. What if I sell in multiple tax regions (like EU + UK)?
You’ll need an integration that supports region-specific tax rules. A2X and Synder offer advanced tax mapping by location, which is key for cross-border compliance.
Reporting and Reconciliation
15. How does integration improve reporting?
By sending summarised, accurate data straight into your P&L and balance sheet. You’ll get clearer gross profit margins, net income tracking, and better insights overall.
16. Can I still use my bank feed in Xero/QuickBooks?
Yes and you should. Integration apps post your payouts, and the bank feed captures your actual deposits. You just match them during reconciliation.
Advanced Settings & Customisation
17. Can I set up different mappings by product type, sales channel, or payment method?
Yes many apps (especially A2X and Synder) support detailed mapping for multiple stores, payment gateways (e.g., Shopify Payments vs PayPal), and even bundles.
18. Can I connect Shopify to both Xero and QuickBooks at the same time?
No. You should only connect Shopify to one accounting platform to avoid duplication and sync conflicts.
Support, Pricing & Getting Help
19. Are the Shopify to Xero/QuickBooks apps free?
Most are subscription-based, with pricing based on order volume. Expect to pay £20–£60/month depending on features and complexity.
20. What kind of support is available if something goes wrong?
Look for apps with live chat, help centres, and responsive email support. If you’re stuck, our team at eSeller Accountant is also just a phone call away.
Final Thoughts: Stop Wasting Hours on Manual Bookkeeping
Integrating Shopify with Xero or QuickBooks isn’t just a time-saver it’s a business upgrade. You’ll reduce human error, automate tedious tasks, and finally trust your numbers at tax time.
But the setup has to be right. Mappings, tax codes, accounts, and reconciliation rules all need to work together.
That’s where we come in. At eSeller Accountant, we specialise in Shopify accounting automation using Xero and QuickBooks. We don’t just connect the dots we set you up for growth, compliance, and peace of mind.
✅ Done-for-you Shopify to Xero/QuickBooks integration
✅ VAT & tax setup that passes HMRC scrutiny
✅ Post-integration support when you need it
Book your free consultation today.Let’s make your numbers work smarter.
