QB Issue Resolution:

If you are using the Sync with Square integration, you should see Invoice and Payments recorded in QuickBooks for each of your sales. Provided these sales were deposited by Square into your bank, the integration will also create a “Deposit” transaction that links these sales together and also adjusts for the fee charged.

This Deposit transaction should match what goes into your bank account exactly. So in the bank feed of your bank account, you can match the deposited amount with this Deposit transaction created by the integration

Resolution for Issue 'I just synced Quickbooks online and Square. My sales are recored and in Undeposited Funds. How do I now match this to my bank deposits and account for the Square fees?' available: Yes (Solved).
Source: Intuit Community forum.

I just synced Quickbooks online and Square. My sales are recored and in Undeposited Funds. How do I now match this to my bank deposits and account for the Square fees?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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