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Managing finances across multiple platforms can be a nightmare for growing eCommerce businesses. Between tracking sales, managing inventory, and reconciling payments, the manual data entry alone can consume hours of your team's time each week.
If you're running a Shopify Plus store and using QuickBooks Online for accounting, there's a better way. The official QuickBooks Online Global app by Intuit automates your financial data flow, eliminating manual entry and reducing costly errors.
This guide walks you through everything you need to know to set up the integration correctly the first time.
Before beginning the setup process, make sure you have:
The integration between Shopify Plus and QuickBooks Online solves several critical business challenges:
Instead of manually entering hundreds or thousands of orders into QuickBooks, the app automatically syncs your sales data on a schedule you define. This eliminates the tedious work of transferring order data between systems.
Automated syncing means your books always reflect your actual sales, refunds, and fees. No more discrepancies between your Shopify reports and QuickBooks statements.
The app maps your Shopify sales taxes to the correct QuickBooks accounts, making tax season and audits significantly less painful.
Payouts sync automatically with transaction details, making it easy to match your bank deposits to the corresponding sales in QuickBooks. This is particularly valuable for B2B manufacturers who may also need to implement custom payment terms like Net 90 or deposits.
As your business grows, the integration scales with you, whether you're processing 100 orders per month or 10,000.
Understanding what data flows between platforms helps you configure the integration correctly:
You can start the connection from either platform:
From Shopify (Recommended):
From QuickBooks Online:
The app is free to install, though you'll need an active QuickBooks Online subscription to use it.
Important: The integration can only be set up once. If you need to reset it later, you'll need to contact Intuit support.
You'll be redirected back to Shopify once the connection is established.
This is the most important part of the setup. Take your time here to avoid issues later.
Option 1: Summary Sync (Recommended for Most Stores)
Why Summary Sync Matters: Shopify reports gross activity (every sale, refund, fee), while your bank only shows net deposits. Summary sync creates entries that match your actual bank deposits, enabling one-click reconciliation instead of hunting through hundreds of individual transactions.
Option 2: Individual Order Sync
The app will ask you to map your Shopify data to QuickBooks accounts. Here's how to set it up correctly:
Income Accounts:
Expense Accounts:
Asset Accounts:
Critical Setup Step: The Shopify Clearing Account is essential for proper reconciliation. This is NOT your actual bank account. It's an intermediate account where sales are recorded before they appear as bank deposits. When payouts hit your bank, you'll match them to this clearing account.
Tip: If you don't see the right accounts, you can create them directly in QuickBooks before continuing the setup. For B2B manufacturers, consider creating separate income accounts for different product categories to improve reporting.
Decide whether you want two-way inventory sync:
One-Way (Shopify → QuickBooks):
Two-Way Sync:
You need to decide how far back to sync historical data:
Options:
Recommendation: If you're mid-fiscal year, sync from January 1st. If it's early in the year, start fresh to avoid complicating last year's books.
Set how often data syncs between platforms:
You can always manually trigger a sync if you need updated data immediately.
Before relying on the integration, run a test:
Problem: Mapping all income to one generic "Sales" account
Solution: Create separate income accounts for products, shipping, and taxes for better reporting
Problem: Importing years of historical orders that overwhelm QuickBooks
Solution: Only sync current fiscal year or start fresh
Problem: Shopify payouts post directly to your bank account, making reconciliation difficult
Solution: Create a Shopify Clearing Account to track the flow from sale to payout
Problem: Customers appear twice in QuickBooks
Solution: Enable customer matching by email address in the app settings
Problem: Individual order sync creating thousands of invoices
Solution: Use summary sync unless you have specific B2B reporting needs
Problem: Only mapping Shopify Payments while also using PayPal or other gateways
Solution: Create separate clearing accounts for each payment gateway to track different settlement schedules
Problem: Not mapping country-specific VAT or sales tax codes
Solution: Configure tax settings for each region where you sell (UK VAT, EU OSS, US state sales tax)
If you operate multiple Shopify stores under Shopify Plus, you have two options:
If you sell internationally and collect multiple currencies:
After your data syncs, you need to reconcile your bank deposits with QuickBooks entries. This is where many businesses struggle.
In QuickBooks:
Important: If using summary sync, this is typically a one-click match. If using individual order sync, you'll need to manually calculate and match the net payout amount.
After each payout cycle:
If your clearing account has a balance:
Check:
Fix: Manually trigger a sync and check error logs
Check:
Fix: Run a payout reconciliation report in the app
Check:
Fix: Perform an inventory count and adjust both systems to match
Check:
Fix: Use QuickBooks' duplicate detection tools or contact support
While the setup is straightforward, consider hiring a QuickBooks ProAdvisor or accountant if:
While the official Intuit app is the most popular choice, alternatives exist:
Webgility: Advanced features for high-volume sellers, multiple sales channels
OneSaas: Good for businesses using multiple apps beyond just Shopify and QuickBooks
A2X: Specialized in eCommerce accounting with excellent reconciliation features
Synder: Strong multi-channel support if you sell on Amazon, eBay, etc.
Each has different pricing and features. The official Intuit app is free but alternatives may offer capabilities worth the cost for complex businesses.
If you're using a different ERP system, you may also want to explore our guides on Shopify ERP Integration, setting up the Acumatica-Shopify Connector, or connecting Microsoft Dynamics 365 Business Central with Shopify.
For most Shopify Plus stores, the answer is absolutely yes. The time saved on manual data entry typically pays for itself within the first month. More importantly, the accuracy improvements reduce costly accounting errors and make tax compliance far less stressful.
Time Savings Example:
A store processing 500 orders per month would need to manually enter each transaction, reconcile monthly payouts, and fix data entry errors. The automation eliminates these repetitive tasks entirely, freeing your team to focus on strategic financial planning instead of data entry.
Setting up the Shopify Plus and QuickBooks Online integration correctly the first time will save you countless hours and headaches down the road. Take the time to understand your account mapping, choose the right sync method for your business, and test thoroughly before going live.
The beauty of automation is that once it's set up correctly, it just works, leaving you free to focus on growing your business instead of managing spreadsheets.
Official Documentation:
Need help with your Shopify Plus integration? Whether you're setting up for the first time or troubleshooting an existing connection, proper configuration is critical to maintaining accurate financial records as you scale.
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