If your employees were set up for Direct Deposit in QuickBooks Online Payroll but suddenly got paid by paper check without you changing anything, you’re not alone. This issue can happen due to account verification problems, expired authorizations, payroll setting changes, or temporary system glitches.
This guide walks you through how to diagnose and fix the problem step by step, and includes helpful tools, tables, FAQs, and interactive elements you can embed in your blog.
Common Reasons Direct Deposit Reverts to Check
| Cause | What Happens | Quick Fix |
|---|---|---|
| Bank account needs re-verification | QBO disables Direct Deposit for safety | Reconnect/verify bank |
| Expired Direct Deposit authorization | Employees switch to paper check | Re-authorize DD forms |
| Payroll processed before DD cutoff time | System defaults to check | Run payroll earlier |
| Employee profile accidentally edited | DD box becomes unchecked | Re-enable Direct Deposit |
| QuickBooks system bug or sync issue | Long-time DD users paid by check | Toggle DD off/on and save |
Step-by-Step Fix
- Open Employee Profile
- Go to Payroll → Employees
- Select the affected employee.
- Check Payment Method
- Click Edit next to Pay method.
- Ensure Direct Deposit is selected.
- Re-enter Bank Details (if needed)
- Re-add routing and account number.
- Save changes.
- Verify Company Direct Deposit Settings
- Go to Payroll Settings → Direct Deposit
- Confirm your company bank account is verified.
- Run a Test Payroll
- Create a small test run (or preview payroll) to confirm DD is active.
Direct Deposit Timing Calculator
Use this to estimate if you’re before the cutoff (2 banking days before payday).
Payroll Cutoff Countdown Timer
Quick Settings Checklist (Dropdown Toggle)
Mini Troubleshooting Quiz
Did you recently update your company bank account?
Reader Poll
Has this happened more than once?
FAQ
This usually happens if your bank account needs re-verification, the employee’s direct deposit authorization expired, or QuickBooks temporarily disabled direct deposit due to a security or sync issue.
Yes. Many users report this after bank updates, failed verification, or system glitches where long-time direct deposit employees are switched to paper check automatically.
Open the employee profile in Payroll, edit the Pay method, select Direct Deposit again, re-enter bank details if required, and save. Also confirm your company bank is verified in Payroll Settings.
Not always. That’s why you should review the payroll preview screen each time before submitting to confirm the payment method shows Direct Deposit.
Run payroll at least two business days early, keep your bank account verified, avoid frequent bank edits, and double-check employee payment methods before every payroll submission.
Best Practices to Avoid Repeat Issues
- Run payroll at least 2 business days before payday
- Re-verify Direct Deposit after any banking change
- Keep employee profiles locked to avoid accidental edits
- Regularly review payroll preview screen before submitting
Final Thoughts
If long-time Direct Deposit employees suddenly get paid by check, don’t panic. In most cases, re-enabling and re-verifying Direct Deposit in both the employee profile and payroll settings resolves the issue quickly. Using checklists, cutoff calculators, and preview reviews can prevent this from happening again.
