To download and sync Shopify transactions into QuickBooks Online, you must link your Shopify store with PayTraQer. This article explains how to integrate Shopify with PayTraQer and sync Shopify orders, products, customers, taxes, discounts, shipping charges, and refunds into QuickBooks Online.

Step 1: Open the Shopify connector in PayTraQer

• Log in to PayTraQer with the QuickBooks Online company you want to sync with Shopify.

• From the left menu, select Connectors.

• Choose E-commerce Connectors to view the online store platforms connected to your PayTraQer account.

• Find your Shopify connection from the list.

• Make sure the Shopify connector is connected and active before moving to the next step.

Step 2: Review how Shopify transactions will be recorded in QuickBooks

• In the Shopify connector row, click See How It Works.

• A User Guide window will open with a quick overview of how PayTraQer syncs Shopify data to QuickBooks Online.

• Stay on the Transaction Recording tab.

• Review how PayTraQer converts each Shopify transaction type into QuickBooks Online entries.

• Check how Shopify payments, invoice payments, bank payouts, refunds, and expenses are mapped in QuickBooks Online.

• Make sure Shopify fees are recorded as expenses where applicable.

• Click OK once you have reviewed the transaction recording flow.

Step 3: Open the Transactions page in PayTraQer

• From the left menu, select Transactions.

• The Transactions dashboard will show different tabs to help you review and manage Shopify transactions before and after syncing.

• Stay in the Review tab to view Shopify transactions that are ready to sync with QuickBooks Online.

• Click Filter to narrow down the Shopify transactions you want to review.

• You can filter transactions using options such as Date, Amount, Payment System, Transaction Type, Transaction Id, and Contact.

• After applying the required filters, select the Shopify transactions you want to process.

• The selected transactions will be highlighted, and the total selected count will appear at the bottom of the screen.

• Click Sync to upload the selected Shopify transactions to QuickBooks Online in bulk.

• Choose Ignore if you do not want to sync the selected Shopify transactions.

• This helps you review and sync multiple Shopify transactions at once instead of processing each record manually.

Step 4: Start the sync review for a Shopify transaction

• Go to the Review tab on the Transactions page.

• Find the Shopify transaction you want to sync.

• Review the transaction type shown on the record, such as Payment, Invoice Payment, Bank Payout, Customer Refund, or Expense.

• Check the mapped QuickBooks entry type displayed on the transaction.

• Review the customer name, transaction date, amount, and transaction ID before syncing.

• Click Review & Sync to open the transaction review panel.

• If you do not want to sync the selected Shopify transaction, click Ignore.

• In the review panel, verify the Shopify transaction details and QuickBooks mapping.

• Check the sales amount, item details, customer details, taxes, discounts, shipping charges, and fees if they are available for the transaction.

• Confirm the clearing account or bank account selected for the Shopify transaction.

• Once the details look correct, click Review & Sync to sync the Shopify transaction into QuickBooks Online.

Step 5: Confirm the synchronization result

• After clicking Review & Sync, PayTraQer will show the Transactions Synced Successfully window.

• Check the sync summary displayed on the screen.

• Make sure the Successful count shows that the Shopify transaction was synced.

• Review the Shopify transaction entry shown in the result window.

• Check the transaction type and amount to confirm that the correct record was synced.

• This confirms that the selected Shopify transaction has been posted to QuickBooks Online.

• Click OK to close the confirmation window.

Step 6: Verify the synced Shopify transaction in PayTraQer

• Go to the Synced tab on the Transactions page.

• Find the Shopify transaction that was posted to QuickBooks Online.

• Click details and Open in QuickBooks to verify the created record directly in QuickBooks Online.

• Use Report if you want to download or review the sync summary.

• If the transaction was synced by mistake, click Undo to reverse the Shopify sync from PayTraQer.

Step 7: Open the Shopify Sync Settings page

• From the left menu, select Settings.

• Choose Sync Settings from the list of options.

• Find the Shopify connector card on the page.

• Click Change Settings to open the Shopify sync configuration.

• Make sure the Shopify settings screen is displayed before making any changes.

• This page allows you to manage how Shopify sales, items, customers, taxes, fees, discounts, shipping charges, and refunds sync with QuickBooks Online.

Sales settings

Accounts

• Bank Account to deposit your sales/income

  • Default: Shopify Bank Account per currency

  • Change when: You keep separate clearing banks by currency or brand

  • Check: Sales and fees land in the same clearing bank

Payment method

• Payment methods to track your transactions

  • Default: Shopify

  • Check: Payment Method shows Shopify on created sales

Separate GL by payment system

• Do you want to configure separate GL accounts for your payment system

  • Default: No

  • Use when: You link additional processors under Connectors → Payment connectors and want different GL routes per processor

  • Check: Posting accounts change based on the payment source

Record the Sales as

• Default: SalesReceipt

• Use when: Switch to Invoice if you bill first and collect later

• Check: New sales use the selected form

Customers

• Create Customer automatically if it does not exist

  • Default: Yes

  • Check: No missing customer errors

• Common Customer for your Sales Transactions

  • Default: Off

  • Use when: You run summaries or do not need per-customer detail

• Customize Customer Matching

  • Use when: Buyer names differ from QuickBooks

  • Check: Repeat buyers map to one customer record

Tracking

• Location/Department and Class

  • Your example: Location set to F05 - Events & Conferences; Class set to Administrative

  • General use: Pick your own Location and Class values if you track them

  • Check: New sales carry the selected values

Sync scope

• Skip the sales and process the associated fees only

  • Default: No

  • Use when: Sales are posted by another system and you only want fee expenses

Products and services Settings

Auto Creation

• Do you want to create Products/Services automatically

  • Default: No in your settings

  • Implication: Every item used by Shopify must already exist in QuickBooks, or you must use a Common Item

  • Tip: If you turn this On, choose the item Type for auto-created items

Type for auto-created items

• Default when enabled: Non-Inventory or Service

Income Account for auto-created items

• Default: Sales

• Check: New items point to the correct income account

Match Product

• Match Product by

  • Default: Name

  • Use when: Switch to SKU if both catalogs have stable SKUs

• Customize Product Matching

  • Use when: Names differ between Shopify and QuickBooks

  • Check: No duplicate items after sync

Common Item

• Use common product/service for all your sales

  • Default: No

  • Use when: You post summaries or do not need item detail

  • Then: Select common product/service to pick the default item

Tax settings

Auto Tax calculation

• Default: Yes to detect and apply tax on synced sales and expenses

Inclusive settings

• Tax Included in Payments

  • Enter the Tax Percentage (%) if your direct payments are tax-inclusive

• Shipping tax percentage

  • Enter the Tax Percentage (%) if shipping is taxable

Default Tax Code

• Tax Code

  • Choose a common code to apply to all transactions when required

  • This overrides automatic detection

• Check: Open a synced sale and confirm the tax code and amount

Fees settings

Core fee setup

• Vendor who receives the Payment Fees: set to Shopify

• Fee Category to record the expenses: choose Shopify Fees or your fee account

• Bank Account to record Payment Fees: Shopify Bank Account per currency

• Separate GL by payment system: keep No unless you want GL by processor

• Class and Location/Department for your Fees: set if you report by these fields

• Skip the fee details from syncing: keep No to capture fee lines

Payouts and settlements Settings

Do you want to process the payouts/settlements

• Default: No

• Turn On to create Bank Transfer transactions from the Shopify clearing bank to your checking account

• Check: Transfers match deposits in your bank feed when enabled

Clearing account vs checking account
The clearing account holds Shopify sales and fees inside QuickBooks.
The checking account is your real bank that receives the payout.
When payouts are on, transfers move money from clearing to checking so the clearing account nets to zero.