QB Issue Resolution:

It looks like your Square deposits are being directly added to your register from the bank feed and not properly matched to the Square Invoice payments. Your Square invoice payments should go to Undeposited Funds first, then you make a bank deposit in QBO of all the Square Invoice payments (less fees) that match the Square bank feed deposits that come into your bank feed.

Resolution for Issue 'My square income transaction report has all our paid invoices, but then there are some transactions labeled “deposit” which is the same payment taken but with the square fee subtracted causing our square income to be overstated. How do I fix this?' available: Yes (Solved).
Source: Intuit Community forum.

My square income transaction report has all our paid invoices, but then there are some transactions labeled “deposit” which is the same payment taken but with the square fee subtracted causing our square income to be overstated. How do I fix this?: 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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