Connect Shopify to QuickBooks Online

• Transaction sync date: The start date for importing Shopify transactions (up to 12 months back). You can manually exclude or undo transactions imported from this period if they were previously entered.
• Add transactions automatically: Enable this to let QuickBooks Online automatically add high-confidence transactions to your books. These appear in the Categorized tab under Integration transactions.
• Product Tracking: Turn ON to track Shopify products in QuickBooks Online. The app attempts to match products by SKU & names with existing ones in QuickBooks Online to avoid duplicates. Close matches appear in the For Review tab with suggested matches. If no match is found, the product isn't automatically added; you will need to manually create in QuickBooks Online. If OFF, all transactions use the default Shopify sales item (changeable in settings).
• Deposit account: The bank account where you receive payouts from Shopify. This can be changed later.
• Payment account: The account (typically a credit card) used if you owe money to Shopify. This can be changed later.

Note: You can modify these settings later by selecting Settings in the Shopify tile.
There are additional Advanced Settings. Default accounts, items, customer and vendors will be created, these can be modified in the App Settings if you have pre-existing accounts you prefer to use. Accounts not in use can be made inactive or merged in your Chart of Accounts.

• Customer: Default customer “Shopify Customer" is used if Customer Tracking is turned OFF in app settings or no match is found.
• Sales Item: Default item “Shopify Sales Item” is used on sales If Product Tracking is turned OFF in app settings or no match is found.
• Shipping: Default item "Shopify Shipping Item”   is used on sales If  Shipping is turned OFF in the QuickBooks Online settings.
• Discounts: Default item "Shopify Discount Item” is used on sales If Discount is turned OFF in the QuickBooks Online settings.
• Sales Tax Payable: Default “Shopify Sales Tax Item”  is used on sales if Automated Sales Tax is turned OFF in QuickBooks Online settings.
• Fees: Account used to record Shopify Fees, selling commission and general payment processing fee. 
• Adjustment: Account used to record any miscellaneous adjustments in Payout. 
• Reserve balance: Account used for any funds held by Shopify 
• Tips: Account used to record tips from sales. 
• Gift Card; Account to record liability for when gift card is sold or used as payment. 
• Hold and disputes: Account used when funds are held by Shopify for potential disputes, chargebacks.

Go to All apps , then Accounting, then Integration transactions (Take me there).

Transactions appear in the following tabs:

• For Review: Contains imported transactions that need your attention before being added to your books.
  • Confirm: Transactions with complete information that can be added quickly. If auto-add is enabled, many transactions bypass this step.
  • Review: Transactions missing details like customer name, product name, or account mapping. Enter the missing info, then confirm the transaction.
• Categorized: Transactions imported and added to your QuickBooks Online books. These transactions appear in your reports.
• Excluded: Transactions imported but manually excluded by you. These transactions do not affect your books or reports. The app does not automatically exclude transactions.

• 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.

Step 1: Review and Confirm Individual Transactions

1. Go to All apps , then Accounting, then Integration transactions (Take me there).
2. Confirm transactions listed with the Confirm action.
3. For transactions listed with the Review action, enter any missing info (customer, product, etc.) and then confirm them.
4. 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.
5. B2B orders in Shopify will be created as Invoice (linked to Company) and if there is payment for the order, Invoice payment is created and linked to Invoice.
   Note: If the invoice is paid in QuickBooks Online, this will update Shopify to mark order as paid.

Step 2: Review and Add the Payout

1. Go to All apps , then Accounting, then Integration transactions (Take me there).
2. Make sure all individual transactions included in the payout show as Categorized.
3. make sure all adjustment lines in the Funds in this payout section have an account selected.
4. Select Add (or Confirm) for the Payout transaction.
5. QuickBooks Online creates a Deposit transaction that moves the net payout amount from Undeposited Funds (or Payments to deposit) to your designated Deposit account (the bank account selected in settings). This deposit automatically includes all the related Sales Receipts, Receive Payments (for B2B transactions) and Expenses confirmed in Step 1. Any adjustments from the Funds in this payout section appear at the bottom of the Deposit transaction.

Step 3: Match in Bank Transactions

1. Go to All apps , then Accounting, then Bank transactions (Take me there).
2. Find the deposit account you selected in the app settings.
3. QuickBooks Online automatically suggests a Match between the bank deposit received from Shopify and the Deposit transaction created in Step 2.
4. Select Match.

The bank transaction is reconciled.

Important: Always add/confirm transactions from the App transactions tab before addressing them in the Bank transactions feed. Do not manually Add the deposit in the bank feed. Always use Match. If no match is found, review Steps 1 and 2 to ensure all transactions were added correctly or contact support.

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.

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.

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.

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

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.

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”.

Payment Status Sync

If a Shopify B2B invoice is marked as paid in QuickBooks Online (e.g., via ACH transfer), the status syncs back to Shopify to keep both platforms updated.

Link to Payouts and Reconciliation

If B2B payments are processed via Shopify Payments, the Invoice Payment and any related fee Expense are automatically included in the deposit created for the payout.

1. Go to Integrations and select Manage integrations (Take me there).
2. Find the Shopify app card.
3. Select the more options icon.
4. Select Disconnect.

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,