Running a Shopify store is exciting, but when it comes to accounting, things can get messy. Tracking sales, processing refunds, handling fees, and staying on top of taxes often means hours of manual work—unless you use the right tools. This is where Shopify QuickBooks integration comes in.
By connecting your Shopify store with QuickBooks Online, you can automate bookkeeping, reduce errors, and get a clear picture of your business’s financial health—all without spending late nights reconciling spreadsheets.
In this guide, we’ll walk you through why integration matters, how to set it up, the best apps to use, and how eSeller Accountant can help you simplify the process.
What is Shopify QuickBooks Integration?
Shopify QuickBooks integration is the process of connecting your Shopify store with QuickBooks Online so that sales, refunds, taxes, fees, and even inventory are automatically synced.
Instead of manually entering every transaction into QuickBooks, the integration pulls data from Shopify and records it in your books—saving time and reducing mistakes.
👉 Think of it as a bridge between your eCommerce platform and your accounting system.
Why Do Shopify Sellers Need QuickBooks Integration?
If you’re selling on Shopify without QuickBooks integration, chances are you’ve experienced at least one of these headaches:
- Manual data entry: Copying transactions into QuickBooks one by one.
- Inaccurate books: Human error during reconciliation.
- Tax season stress: Scrambling to separate sales, VAT, and expenses.
- Cash flow blind spots: Not knowing your real profit until it’s too late.
With Shopify QuickBooks Integration, you get:
✅ Automated accounting – Shopify orders flow directly into QuickBooks.
✅ Accurate tax tracking – Sales tax and VAT recorded correctly.
✅ Smarter reporting – Real-time insights into sales, profit, and cash flow.
✅ Simplified reconciliation – Marketplace fees, shipping, and refunds are captured.
✅ Scalability – Grow your store without drowning in bookkeeping tasks.
📌 As accountants who specialize in eCommerce, we’ve seen clients save up to 15 hours per month simply by automating Shopify bookkeeping with QuickBooks Online.
How to Integrate Shopify with QuickBooks Online
Good news: integrating Shopify with QuickBooks Online is simpler than most people think.
Here’s a step-by-step guide:
- Choose your integration method
- Use QuickBooks Connector (by Intuit), or
- Select a third-party app like A2X, Webgility, or Synder.
- Log into QuickBooks Online
- Go to Apps in the left-hand menu.
- Search for Shopify.
- Connect Shopify
- Install the app.
- Grant permissions for data sharing between Shopify and QuickBooks.
- Map your accounts
- Assign Shopify sales to the right income account.
- Map fees, shipping, and refunds correctly.
- Set up tax settings
- Sync Shopify tax rules with QuickBooks for accurate reporting.
- Test the sync
- Import a few transactions.
- Check if everything lands in the right accounts.
- Go live
- Enable automatic syncing.
- Review your QuickBooks dashboard regularly for accuracy.
👉 Pro Tip: Always test with a few sample transactions before letting the app sync all your data.
Best Apps & Tools for Shopify QuickBooks Integration
There’s no one-size-fits-all solution—your choice depends on store size, transaction volume, and reporting needs.
Here are the top apps:
| App | Best For | Pros | Cons |
|---|---|---|---|
| QuickBooks Connector (by Intuit) | Small to mid-size stores | Direct integration, reliable | Limited customization |
| A2X | Amazon/eBay + Shopify sellers | Accurate, tax-friendly, great for accountants | Higher cost for big volumes |
| Webgility | Growing eCommerce businesses | Advanced features, multi-channel | Can feel complex |
| Synder | High transaction volume | Handles multi-currency, detailed sync | Monthly fees add up |
| Bold Commerce | Shopify-first sellers | Deep Shopify integration | Limited outside Shopify |
⚡Many of our eSeller Accountant clients prefer A2X because it handles marketplace settlements (Shopify Payments, PayPal, Stripe) with precision.
Common Challenges & How to Solve Them
Even with great tools, you might run into some issues. Here’s how to handle them:
1. Data Sync Issues
- Problem: Transactions don’t match in QuickBooks.
- Solution: Double-check account mappings in the integration settings.
2. Duplicate Entries
- Problem: Sales appear twice.
- Solution: Ensure you’re not manually entering data while the sync is active.
3. Multi-Currency Complications
- Problem: Selling globally causes mismatched exchange rates.
- Solution: Use apps like Synder or A2X, which support multi-currency.
4. Refund & Return Handling
- Problem: Refunds not matching correctly.
- Solution: Map refund accounts properly during setup.
How eSeller Accountant Can Help
At eSeller Accountant, we specialize in helping Shopify sellers with accounting, bookkeeping, and integrations.
Here’s how we can support you:
- ✅ Seamless Shopify QuickBooks Online setup – We connect your store and map everything correctly.
- ✅ Clean-up & migration – Fix messy books and migrate from other software.
- ✅ Ongoing support – Troubleshoot sync issues, tax settings, and reconciliations.
- ✅ eCommerce expertise – We understand Shopify fees, PayPal payouts, and marketplace settlements.
👉 If you want to spend less time on bookkeeping and more time growing your store, we’re here to help.
FAQs About Shopify QuickBooks Integration
1. How do I connect Shopify with QuickBooks Online?
Go to QuickBooks Online → Apps → Search “Shopify” → Install → Connect accounts → Map sales, fees, and taxes → Enable sync.
2. Can QuickBooks automatically sync with Shopify?
Yes. With QuickBooks Connector or third-party apps like A2X or Synder, transactions sync automatically on a schedule you set.
3. What is the best app for Shopify QuickBooks integration?
It depends. Small stores can use QuickBooks Connector. Larger or multi-channel sellers often choose A2X or Synder.
4. Do I need QuickBooks Online for Shopify integration?
Yes. QuickBooks Online is cloud-based and integrates directly. QuickBooks Desktop requires extra steps or middleware.
5. How much does Shopify QuickBooks integration cost?
QuickBooks Connector is free with QuickBooks Online. A2X, Webgility, and Synder have monthly fees starting around $19–$49, depending on transaction volume.
Conclusion
Accounting shouldn’t hold you back from scaling your Shopify store. With Shopify QuickBooks integration, you can automate bookkeeping, ensure tax compliance, and always know where your business stands financially.
Whether you’re a small store owner or a fast-growing eCommerce brand, connecting Shopify and QuickBooks is one of the smartest investments you can make.
💡 And if you’d rather not deal with setup headaches, eSeller Accountant is here to help you get it right the first time.
