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Connect Shopify to QuickBooks Online
Learn how to connect Shopify to QuickBooks Online.
Import transactions and related details automatically from your Shopify account into QuickBooks Online with the Shopify Connector by QuickBooks app. This helps you reconcile your Shopify sales, refunds, fee and payouts accurately and efficiently.
Connect your Shopify store to your QuickBooks Online account to save time by automatically downloading your transactions into QuickBooks. In this video, we'll show you how to connect your account and how to use the app in QuickBooks.
Video transcript
[0:00] If you use Shopify to process your sales, you can save time by automatically downloading your sales and other transactions into QuickBooks. First let's review how to connect your Quickbooks account with the Shopify Connector App. If the permissions look good, click Install once again and click Continue to connect the accounts.
[0:23] From here, you will select which bank account Shopify deposits your money into. This is usually your checking or operating bank account. Keep in mind, Shopify doesn't deposit each sale right away. Instead, you receive a payout from Shopify each day or when you choose to make the transfer.
[0:41] That means you need an account to track where Shopify holds the money before they send you the final deposit that could include sales, refunds, and fees from an entire day's worth of transactions. In QuickBooks, your Undeposited Funds account, which could also say Payments to Deposit, is where Shopify stores your funds before you receive the deposit to your bank.
[1:03] Keep in mind, If you ever need to change the settings, select the three dots on the Shopify app and click Settings. You can see all the default settings that the Shopify Connector uses for line items, customers, vendors, among other things. To change any of these default settings or any of your previous selections, choose a section, make your changes, select Save, and Sync Now.
[1:27] Let's review a few of the ones you should know: Automatically add transactions - allows us to add transactions to your books if we have all the information or we have high confidence. Product tracking - Enables us to match product/service data imported from Shopify with existing products/services in Quickbooks Online.
[1:48] If this setting is OFF, then all products/services from Shopify will be mapped towards a default product, which can be modified in settings. Customer tracking - Similar to Product tracking, this setting will allow us to match customer data from Shopify to existing customer list in Quickbooks Online. If OFF, default customer details will be chosen.
[2:09] Review and confirm the sync settings and click Sync now. Once the sync is complete, you'll see your transactions start to populate. So now, let's add your first sale. Data brought in through the connector can be reviewed before it's added to the books by going to App Transactions or Integration Transactions under Accounting App.
[2:31] Recording transactions from the Shopify integration is an important first step before these transactions can be matched in your bank transactions. Transactions listed under the For Review tab await your approval and don't appear on your reports or financial statements until you confirm them.
[2:50] Click on the transaction if you want to see details of the order like customer information or products sold. If the product needs to be categorized, matched, or created to match your inventory in Quickbooks, you can do this here. If you'd prefer to only see your payouts here, select the filter and then """Payouts."
[3:09] When you see "Review" in the actions column, there may be some information, such as the customer or the product or service, missing. So let's select Review to see additional details about a transaction. If you see "confirm" in the actions column, that means Quickbooks collected all of the necessary information for this transaction.
[3:30] If you would prefer to not review the transaction, select the dropdown menu under the actions column, then "Confirm." You find confirmed transactions in the Categorized tab. They stay here unless you undo them, which moves them back to the For Review tab. Once you click on a transaction, you can either add a new customer or match the customer with a name from Quickbooks.
[3:54] To add this customer as a new customer, select "add new" under the Customer dropdown. QuickBooks fills out all of the information for you based on the information in the "shopify details" box. Select Save. Now let's look at the Products and Services box. Quickbooks shows the Product or Service as a "Shopify sales item" when the Product tracking setting is OFF.
[4:15] When it's ON, it automatically matches existing available products in Quickbooks. If you wish to change this, select the dropdown menu and then select a different product or service. To add a new product or service that matches the description from Shopify, select Add new. Select an income account for this product or service, then Save and Close.
[4:37] Once all of the details of the transaction have been reviewed, select Confirm. QuickBooks will learn from your selections and assign the same product or service to other transactions with the same item. When you have Shopify B2B sales or sales to wholesale customers, those orders will be imported to Quickbooks as Invoices.
[4:58] These invoices will have all the necessary information like products and services sold, company information and payment terms. Say after a few days you get payment for the order in Shopify, it will be imported as an Invoice payment to Quickbooks and the Invoice Payment will be automatically linked to the earlier Invoice that was added to QBO.
[5:19] When a payment for a B2B order happens outside of Quickbooks and you mark the invoice as Paid, then this Invoice status (paid) will be sent to Shopify and the order will be marked as paid in Shopify as well. Thereby both Quickbooks and Shopify are in sync for both B2B and B2C transactions. Now that you've added a few sales, go back to the Chart of Accounts.
[5:42] Notice, your bank account balance is still $0.00 because you haven't received the money from Shopify yet. However, your Undeposited Funds or Payments to Deposit account balance shows where the sales will sit until you receive the payout from Shopify. When you receive money from Shopify to your bank account, QuickBooks records a deposit. Let's review a payout transaction now.
[6:06] This transaction will group received payments, fees, and refunds that represent the net payout you receive from Shopify.. Make sure you assign the right bank account, and that it's linked to to correct transactions…and Confirm it. Back on the Chart of Accounts, you see that Undeposited Funds or Payments to Deposit is $0.00, and your bank balance shows the money Shopify deposited.
[6:32] Now you're ready to use the Shopify Connector App in QuickBooks.
Connect the Shopify Connector by QuickBooks app
Prerequisites
A QuickBooks Online account.
Your Shopify shop name (my-store.myshopify.com). (This is the original shop URL generated by Shopify, not your custom URL.)
Shopify user ID and password.
Permissions in Shopify to install third-party apps.
Steps
Sign in to your QuickBooks Online account.
Select Integrations
, then Find integrations (Take me there).Find the “Shopify Connector by QuickBooks” app.
Select Get integration now.
Enter your Shopify store URL (my-store.myshopify.com)
Sign in to your Shopify account, then select authorize access to share data between Shopify & QuickBooks.
Note: You will be redirected to the Review your app settings page in QuickBooks Online. You can set the following:Choose the date you want the app to start importing orders from. You can import transactions from up to one year ago.
Select Deposit account to choose which account payouts are recorded to in QuickBooks.
Select Payments account to choose which account negative payouts are recorded from in QuickBooks.
Select Add transactions automatically to auto post transactions in QuickBooks Online. If left off transactions will require review.
Select Product Tracking to sync products sold on Shopify to inventory items in QuickBooks Online.
Select Customer Tracking to sync customer details from Shopify in QuickBooks Online.
Select Sync now to finish the connection.
Once connected, select Go to Integration Transactions.
Note: The app is now connected. QuickBooks Online will begin importing your Shopify transactions based on the date you selected. The initial import may take between 10 minutes and 3 hours, depending on the volume of transactions. Transactions import in batches, so allow up to 3 hours for large volumes to complete fully.
Terminology
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.
Find your transactions
Go to All apps
, then Accounting, then Integration transactions (Take me there).
Categories
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.
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.
Reconcile Shopify transactions in QuickBooks Online
Step 1: Review and Confirm Individual Transactions
Go to All apps
, then Accounting, then Integration transactions (Take me there).Confirm transactions 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 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
Go to All apps
, then Accounting, then Integration transactions (Take me there).Make sure all individual transactions included in the payout show as Categorized.
make sure all adjustment lines in the Funds in this payout section have an account selected.
Select Add (or Confirm) for the Payout transaction.
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
Go to All apps
, then Accounting, then Bank transactions (Take me there).Find the deposit account you selected in the app settings.
QuickBooks Online automatically suggests a Match between the bank deposit received from Shopify and the Deposit transaction created in Step 2.
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.
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.
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.
Shopify B2B Transactions in QuickBooks Online
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.
Disconnect the app
Go to Integrations
and select Manage integrations (Take me there).Find the Shopify app card.
Select the more options
icon.Select Disconnect.
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.
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