QB Issue Resolution:

Are you using a .iif file, then?

Because the .qbo file treats them as Checks and deposits.

For debits and credits, Deposits will Debit a bank account and Checks will credit a bank account; that is the Accounting Perspective, as opposed to the consumer’s view. .iif will give the Accounting perspective.

Resolution for Issue 'When downloading bank transactions, columns are labeled Increase and Decrease. Deposits are going to the decrease column and purchases are going to the increase column.' available: Yes (Solved).
Source: Intuit Community forum.

When downloading bank transactions, columns are labeled Increase and Decrease. Deposits are going to the decrease column and purchases are going to the increase column.: 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 Accounting perspective
Quickbooks Repair Pro will resolve it efficiently and affordably. Guaranteed resolution of your issue, or you pay nothing!

Error Recovery for Accounting perspective [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: