QB Issue Resolution:

It’s possible that you’re using the main bank account for your payroll transactions, that’s why it’s showing two transactions in the register.

Also, please ensure that you’ve set up the correct linked bank account for your payroll transactions in QuickBooks Online (QBO). Next, compare the two transactions that is showing in the register especially the bank accounts used.

Resolution for Issue 'Boss was doing QB payroll as normal by check. He started transferring his payroll money into linked bank account. Why does it looks like 2 transactions in register?' available: Yes (Solved).
Source: Intuit Community forum.

Boss was doing QB payroll as normal by check. He started transferring his payroll money into linked bank account. Why does it looks like 2 transactions in register?: 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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