QB Issue Resolution:

the work flow is to enter the invoice
receive payments against the invoice

then download from the bank and match the download transaction to the QB transaction

it sounds like when you do the download you are assigning the deposit transaction to the income account, when it should match the receive payment/deposit in QB

Resolution for Issue 'My profit and loss report in cash basis shows both deposits and invoices. It is doubling my sales income number. How do I fix this?' available: Yes (Solved).
Source: Intuit Community forum.

My profit and loss report in cash basis shows both deposits and invoices. It is doubling my sales income number. 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.

Support for Cash basis
Quickbooks Repair Pro will resolve it efficiently and affordably. Guaranteed resolution of your issue, or you pay nothing!

Error Recovery for Cash basis [Canada]
E-Tech is the #1 Quickbooks data migration and Conversion service provider.

Get 50% off Quickbooks Online

Click Here for 50% off!

Additional Support Options: