Direct deposit employess being issued checks on last run without asking

CreativePrinters · ‎January 30, 2026

This is a first and I'm not going to bother asking why. I would like to know how to edit or undo it.

I can delete these paychecks, but the warning it gives me doesn't makes sense to me.

"Any refunds or carry forwards of tax withdrawals will be processed after 5 business days from the tax withdrawal date. To get a refund, contact us."

I don't believe that applies to anyone here, but how can I double check?

I can, and probably will, just print the checks since it's only a few, but still a solution would be nice.

CreativePrinters

"voiding a paycheck zeros out the amount but does not reverse the direct deposit or cancel the transferred funds. The Automated Tax Withdrawals will be applied to future payroll runs. "

It wasn't direct deposited, which is the problem. I thought that would be clear. Sounds like I'm better off continuing with printing and issuing the checks. Wouldn't want to double dip on taxes.

I believe I figured out what started this, though. When I first ran it it defaulted to the previous payroll period which wasn't run as I have the only hours for that period and I don't pay myself every payroll. So presumably because I was running between the two payroll run dates (before the 1st so it would issue on Monday), it was thus past dated to the previous periods run date (the 16th) which can't be done via direct deposit so it switched to checks. I changed to the current period and Friday's date, but it looks like the pay method stayed stuck on check. Would be great if that would revert back or warn that direct deposit employees are being issued checks when running the current period (hint-hint), but I suppose I will have to remember to watch for that in the future.

Also, I am not going to do auto anything if I have the choice. And certainly not "AI", no thank!

View solution in original post

Irene R

Hello, CreativePrinters.

Have you set up Auto Payroll for your QuickBooks Online (QBO) account? If so, this explains why the paycheck was automatically processed for that pay run and encountered the prompt message. We can review your payroll settings to check if Auto Payroll is enabled and turn it off if you prefer not to run payroll automatically. Here’s how:

Go to the Gear icon, then select Payroll Settings.
Navigate to the Auto Payroll section, then click the pencil icon to edit.
Choose the employee for whom you want to disable Auto Payroll.
Click Done when finished.

Regarding the prompt message, this typically appears after you void a paycheck. Keep in mind that voiding a paycheck zeros out the amount but does not reverse the direct deposit or cancel the transferred funds. The Automated Tax Withdrawals will be applied to future payroll runs. If you need to request a tax refund, our QBO Payroll live support team is available to assist.

As for the employee who received the funds, you can establish an internal agreement on whether they will return the money or have it applied to the next pay run. If they choose to keep the funds, you can make adjustments in the next payroll to account for the correction.

Let us know if you have any further questions about processing QuickBooks direct deposit paychecks.

CreativePrinters

"voiding a paycheck zeros out the amount but does not reverse the direct deposit or cancel the transferred funds. The Automated Tax Withdrawals will be applied to future payroll runs. "

It wasn't direct deposited, which is the problem. I thought that would be clear. Sounds like I'm better off continuing with printing and issuing the checks. Wouldn't want to double dip on taxes.

I believe I figured out what started this, though. When I first ran it it defaulted to the previous payroll period which wasn't run as I have the only hours for that period and I don't pay myself every payroll. So presumably because I was running between the two payroll run dates (before the 1st so it would issue on Monday), it was thus past dated to the previous periods run date (the 16th) which can't be done via direct deposit so it switched to checks. I changed to the current period and Friday's date, but it looks like the pay method stayed stuck on check. Would be great if that would revert back or warn that direct deposit employees are being issued checks when running the current period (hint-hint), but I suppose I will have to remember to watch for that in the future.

Also, I am not going to do auto anything if I have the choice. And certainly not "AI", no thank!

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Direct deposit employess being issued checks on last run without asking