Why is my direct deposit not working in QuickBooks? In this post, we will cover some of the most common QuickBooks Direct Deposit Issues and offer solutions to get you back on track. However, sometimes issues can arise with QuickBooks Direct Deposit, leaving you scrambling to figure out what went wrong. QuickBooks is a popular accounting software that simplifies payroll processing and makes it easy to deposit payments directly into your employees' bank accounts. As a small business owner, one of the most important tasks that you need to handle is paying your employees accurately and on time.