How to Connect and Manage Shopify Transactions in QuickBooks Online?

Managing Shopify sales, payouts, refunds, and fees manually can become difficult as your e-commerce business grows. To simplify bookkeeping and improve accuracy, many businesses choose to connect and manage Shopify transactions in QuickBooks Online. This integration helps automate transaction syncing, reduce manual data entry, and keep your financial records organized in one place.

By connecting Shopify with QuickBooks Online, you can efficiently track sales activity, reconcile payouts, and manage your e-commerce accounting workflow with greater accuracy. In this guide, you’ll learn how to connect and manage Shopify transactions in QuickBooks Online step by step.

What are Shopify Transactions in QuickBooks Online? 

Shopify transactions in QuickBooks Online refer to the sales and payment activities imported from your Shopify store into QuickBooks through the Shopify Connector integration. These transactions help e-commerce businesses track and manage their financial data automatically without relying on manual bookkeeping.

When you connect Shopify with QuickBooks Online, the integration syncs important transaction details such as:

• Sales receipts and customer payments
• Shopify payouts and deposits
• Refunds and returns
• Payment processing fees
• Taxes collected on orders
• Expenses and adjustments related to payouts

These transactions are recorded in QuickBooks Online to help maintain accurate financial reports, simplify reconciliation, and keep your accounting records updated. By managing Shopify transactions in QuickBooks Online, businesses can save time, reduce errors, and streamline e-commerce accounting processes.

How to Connect the Shopify Connector to the QuickBooks app

To connect your Shopify store with QuickBooks Online, you’ll need an active QB Online account, your Shopify store URL, and permission to install apps in Shopify. Proceed with the detailed steps mentioned below:  

Prerequisites

• Make sure you have a QuickBooks Online account. 
• The Shopify shop name (my-store.myshopify.com). (This is the original shop URL generated by Shopify, not your custom URL.)
• Keep the Shopify user ID and password noted somewhere. 
• Allow the permissions in Shopify to install third-party apps.

Steps

• Sign in to your QuickBooks Online account. 
• Go to Integrations and then select Find integrations.
• Look for the “Shopify Connector by QuickBooks” app.
• Click on Get integration now.
• Enter the Shopify store URL (my-store.myshopify.com) of your shop. 
• Sign in to your Shopify account, then choose ” Authorise Access “ to share data between Shopify & QuickBooks.
• Pick the date from which you want the app to begin importing orders (you can go back up to one year). 
• Choose the Deposit account to decide where payouts will be recorded in QuickBooks. 
• Select the Payments account to determine where negative payouts will be deducted from in QuickBooks. 
• Turn on Add transactions automatically if you want transactions to post automatically in QBO; otherwise, they’ll need manual review. 
• Enable Product Tracking to sync Shopify products with inventory items in QBO. 
• Enable Customer Tracking to bring customer details from Shopify into QBO.
• Click Sync now to complete the setup. 
• When done, choose Go to Integration Transactions.

Note: The app connection is complete. QuickBooks Online will start importing your Shopify transactions from the date you selected. The first sync can take anywhere from 10 minutes to 3 hours, depending on how many transactions need to be imported. Since data is brought in batches, larger volumes may require the full 3 hours to finish.

Note: You’ll be taken to the Review your app settings page in QuickBooks Online, where you can configure the following options:

1. Terminology

• Transaction sync date: Set the starting point for importing Shopify transactions (up to the past 12 months). If needed, you can later exclude or reverse any entries from this period if they were already recorded.
• Add transactions automatically: Turn this on to allow QuickBooks Online to automatically post high-confidence transactions. These will appear under the Categorized tab within Integration transactions.
• Product Tracking: Enable this to sync Shopify products with QuickBooks Online inventory. The system tries to match items using SKU and names to avoid duplicates. Suggested matches show in the For Review tab. If no match is found, you’ll need to create the product manually. If disabled, all sales use the default Shopify sales item (which can be updated in settings).
• Deposit account: Select the bank account where Shopify payouts are deposited. This can be updated later.
• Payment account: Choose the account (usually a credit card) used when you owe money to Shopify. This is also editable later.

Note: You can revisit and change these preferences anytime by selecting Settings in the Shopify tile.

2. Advanced settings

Additional default accounts, items, customers, and vendors are automatically created. If you already have preferred accounts, you can update them in the app settings. Unused accounts can be deactivated or merged in your Chart of Accounts.

• Customer: Uses the default “Shopify Customer” if Customer Tracking is disabled or no match is found.
• Sales Item: Uses “Shopify Sales Item” when Product Tracking is off, or no match exists.
• Shipping: Uses “Shopify Shipping Item” if shipping is disabled in QuickBooks Online.
• Discounts: Uses “Shopify Discount Item” if discount tracking is turned off.
• Sales Tax Payable: Uses “Shopify Sales Tax Item” if automated sales tax is disabled.
• Fees: Account for recording Shopify fees, commissions, and processing charges.
• Adjustment: Account for miscellaneous payout adjustments.
• Reserve balance: Tracks funds temporarily held by Shopify.
• Tips: Records tips received from sales.
• Gift Card: Tracks liability when gift cards are issued or redeemed.
• Hold and disputes: Used for funds held due to disputes or chargebacks.

4. Find your transactions

• Navigate to All apps. 
• Choose Accounting. 
• Click on Integration transactions.

4. Categories

Transactions are organized into the following tabs in QuickBooks Online:

• For Review: This tab includes imported transactions that require your approval before they’re added to your records.
  • Confirm: Entries that already have complete details and can be added quickly. If auto-add is turned on, many of these may skip this step.
  • Review: Entries are missing key information, such as customer details, product names, or account mapping. You’ll need to fill in the gaps before confirming them.
• Categorized: These are transactions that have already been added to your books. They are included in your financial reports.
• Excluded: Transactions you’ve chosen to leave out. They won’t impact your books or reports, and none are excluded automatically—you must do this manually.

5. Transaction types

• Payment Received: Individual sales transactions (card, cash, gift card, etc.). The payment type is noted in the description. Details like fees, gross amount, shipping, discounts, taxes, and products/services are imported. Select Review or the transaction row to see details.
• Refund: Individual refund transactions. Details like amount, taxes, and products/services are imported.
• Payouts: Disbursements from Shopify, typically covering sales over a 1-day period (or longer if selected). Shopify collects funds, deducts fees and adjustments, and sends the net amount to your deposit account. A payout includes multiple sales and adjustments from that period.
  • Included transactions: Lists the individual sales within the payout, showing their status: For review, Categorized, or Excluded.
  • Funds in this payout: Shows adjustments made by Shopify. Some are automatically mapped to accounts, while others require manual selection. You can edit how payouts are mapped.

6. Reconcile Shopify transactions in QuickBooks Online

Regular reconciliation helps ensure your Shopify payouts match the transactions recorded in QuickBooks Online. 

a. Review and Confirm Individual Transactions

• Navigate to All apps. 
• Select Accounting and click on Integration transactions.
• Confirm transactions that are listed with the Confirm action.
• For transactions listed with the Review action, enter any missing info (customer, product, etc.) and then confirm them.
• When a Payment received transaction is confirmed, QuickBooks Online creates a Sales Receipt (for sale details) and an Expense (for fees). Both are recorded in the Undeposited Funds or Payments to deposit account. This account acts as a temporary holding account until the payout is processed.
• B2B orders in Shopify will be created as an Invoice (linked to the Company), and if there is payment for the order, an Invoice payment is created and linked to the Invoice.

Note: If the invoice is paid in QuickBooks Online, this will update Shopify to mark the order as paid.

b. Review and Add the Payout

• Navigate to All apps, then select Accounting, and open Integration transactions (Take me there).
• Verify that every individual transaction included within the Shopify payout is marked as Categorized.
• In the Funds in this payout section, confirm that each adjustment entry has an assigned account.
• For the payout transaction, select Add or Confirm.
• After confirmation, QuickBooks Online automatically generates a Deposit transaction that transfers the net payout amount from Undeposited Funds (or Payments to deposit) into the deposit account chosen in your settings. This deposit combines all associated Sales Receipts, Receive Payments for B2B orders, and Expenses that were confirmed in Step 1. Any adjustment entries listed under Funds in this payout are displayed at the bottom of the generated Deposit transaction. transaction.

c. Match in Bank Transactions

• Go to All apps, then choose Accounting, followed by Bank transactions.
• Locate the same deposit account that was selected in the app settings.
• QuickBooks Online should automatically recommend a Match between the bank deposit received from Shopify and the Deposit transaction created during Step 2.
• Select Match to connect the transactions.
• Once matched, the bank transaction is successfully reconciled in QuickBooks Online.

Important: Always review and add or confirm transactions from the App transaction tab before working with items in the Bank transactions feed. Avoid manually selecting Add for Shopify ” directly from the bank feed. Instead, always use the Match option whenever it is available. If QuickBooks Online does not display a suggested match, revisit Steps 1 and 2 to confirm that all transactions were properly added and categorised, or contact support for additional assistance.

7. Sales taxes

The QuickBooks Online Connector automatically tracks and records taxes collected by Shopify on your behalf. This makes sure your payout deposits match your bank records and your sales tax liability remains accurate.

a. Recording marketplace taxes

When you sell through the Shop app, Shopify often pays marketplace sales tax directly to the appropriate authorities before sending you the proceeds. In Shopify payout reports, these are given labels like “Marketplace taxes.”

After you make a sale through the Shop app, the QuickBooks Online Connector imports sales tax information, then identifies the marketplace sales tax and charges it to the Sales Tax Payable liability account. These charges are given labels like “Shopify sales tax item.”

When you get the payout, the QuickBooks Online Connector adjusts the Sales Tax Payable liability account to balance the account with the marketplace taxes withheld by Shopify. When you open the Review, you’ll see this adjustment under Funds in this payout.

Note: By default, marketplace taxes are assigned to the Sales Tax Payable account. You can change this in your settings or for individual payouts.

b. Recording merchant-liable taxes

When you’re responsible for taxes instead of Shopify, the QuickBooks Online connector automatically accounts for them based on how much you owe in your sales location. We record the taxes you’re responsible for in the sales receipt’s Sales tax rate section.

Note: We automatically charge the amount to the appropriate tax agency account for your location.

8. Shopify B2B Transactions in QuickBooks Online

This integration allows you to manage both your retail (DTC) and wholesale (B2B) sales side-by-side.

a. Invoices

When a B2B order is placed in Shopify, it is imported to QuickBooks Online as an Invoice containing all essential data:

• Order Details: All products, services, quantities, rates, and applicable taxes or discounts are recorded in the Invoice.
• Company Profiles: Unlike DTC transactions where customer information is recorded on the transaction, for Shopify B2B orders “Company” information is recorded on the Invoice. The imported company details include the company name, billing address, email, phone number, and website.
• Payment Terms: Terms such as “Net 30” or “Net 60” are imported from the Shopify Order and applied to the corresponding Invoice in QuickBooks Online.
• Identification Tags: To help you stay organized, orders include the Shopify Order Number and Purchase Order (PO) Number. 
• Customer Segmentation: Shopify B2B Companies are imported as Customers and automatically assigned the customer type “Shopify B2B company” for easy reporting.

b. Invoice Payments

If a B2B order is paid through Shopify, an Invoice Payment is created in QuickBooks Online.

• Automatic Linking: If the corresponding invoice is already recorded in QuickBooks Online, the payment will link to it automatically.
• Receive Payment: Once a payment is confirmed, QuickBooks Online creates a “Receive Payment” transaction against the linked invoice.
• Fees: If Shopify charges a payment fee, an Expense is created for that fee in addition to the payment record.

Note: If you see “No invoice found,” the corresponding invoice may still be in the For Review tab. Confirm the invoice first, or manually link it by clicking “Select a different invoice”.

9. Disconnect the app

• Go to Integrations in QuickBooks Online. 
• Select Manage integrations.
• Find the Shopify app card.
• Select the three-dot menu icon.
• Select Disconnect.

10. Get help

If you need support for the Shopify Connector app:

• Live Chat: Select the chat icon in the Shopify app tile on the Integration transactions tab.
• Email: Contact the team qbo-integrationsupport@intuit.com 
• Give Feedback: Select the Give Feedback button on the Integration transactions tab, then the Shopify app.

Conclusion

Finally, we are ending this detailed blog here! We have covered how you can create and manage Shopify transactions in QuickBooks Online. The best way to accomplish that is using the official Shopify Connector by QuickBooks (formerly OneSaas) to automate sales, fees, and payouts.

Hopefully, this information has helped you easily manage your Shopify transactions in your accounting software. For more details, you must contact QuickBooks ProAdvisors at 866-500-0076. Dial the toll-free number to connect with a certified ProAdvisor today!

Frequently Asked Questions

Can I connect Shopify to QuickBooks Online?

Yes, you can connect Shopify to QuickBooks Online to automatically sync sales, inventory, and transaction data. The integration can be done directly via the official QuickBooks Shopify Connector app, or by using third-party apps like A2X or Synder for more complex accounting needs.

How to connect bank accounts and manage imported transactions in QuickBooks Online?

Connecting bank accounts in QuickBooks Online (QBO) automates bookkeeping by importing transactions directly to the Banking or Transactions menu. Users can connect via the “Connect account” button, securely logging into their financial institution to download up to 90 days of historical data.

How to reconcile Shopify in QuickBooks Online?

Reconciling Shopify in QuickBooks Online (QBO) involves matching imported Shopify sales and fees to actual bank deposits using a clearing account. Using the Shopify Connector app by Intuit, you match the net payout in the bank feed to the detailed sales transactions, ensuring the clearing account balance hits zero.

How do I connect Shopify to QuickBooks Online?

Connecting Shopify to QuickBooks Online is done by installing the Shopify Connector by QuickBooks app directly within QuickBooks Online. This automates syncing sales, products, and fees.