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Sync Payment for orders from Shopify into QuickBooks using Webgility Desktop

This article explains how Webgility Desktop users can automatically sync payment updates from Shopify to QuickBooks Desktop using Webgility Desktop. In many cases, orders downloaded from Shopify are initially marked as unpaid but are later paid through the sales channel. By configuring Webgility Desktop to update the payment status of these orders in QuickBooks Desktop, users can ensure that their invoices reflect accurate payment information. This automation helps maintain clean books, supports accurate receivables tracking, and simplifies bank reconciliation.

 

Note: This option is available for invoice-type transactions only.

 

Key Benefits

  • Simplify bank reconciliation by matching QuickBooks Desktop payments to actual deposits.

  • Ensure accurate accounts receivable by reflecting correct outstanding.

  • Gain better visibility into partial, full, or split payments across orders.

 

Setting up the feature

1). In Webgility Desktop navigate to Connections in menu options, then goto Accounting/POS/ERP and click on Sync Settings.

2). Enable Record payment from Sales Channel

  • Under Orders section goto Posting Rules goto Select the transaction type for posting orders and then click on Setup, then under Term Type select “Use Transaction Terms”, then enable Record Payments by enable the box and configure “Each payment as received from Sales Channel” under Record Payment from Sales Channel as.

  • Now click on Save and then Save and Continue.

 

Note: If you have opted for any transaction posting rule then you will need to configure this for each transaction setup separately.

 

3). Enable Order updates feature to detect Payment.

  • Now navigate to Connections again and goto Sales Channel and click on Settings. Then goto Order Processing tab and look for “Check for order updates after download”.

  • Click on Yes radio button for “Check the Sales Channel for any order updates after downloading to Webgility” and then click on Options

  • This will open a popup and show you some preset conditions for detecting the updates. So enable “Payment Details” and click on Save. Then click on Save and Continue.

 

4). Verify payment sync

  • If an existing unpaid order in Webgility Desktop is marked paid at Shopify, while downloading new orders it will detect the update related to payment and move the order to the Updates tab.

  • Navigate to Updates tab, select the order and click on Accept, and this will create the payment against the invoice for the respective order in QuickBooks Desktop.