Running payroll is essential, but what if you need to pause a payroll due to cash flow issues, business restructuring, or seasonal downtime? Don’t worry! QuickBooks makes it flexible for employers to manage payroll timing with ease. Whether you’re using QuickBooks Online Payroll or Desktop Payroll, this guide breaks down the steps to pause a payroll temporarily without penalties or confusion.
For personalized help, call +1-866-409-5111 and speak with a payroll expert today.
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There are several valid reasons to consider putting a temporary stop on payroll:
Seasonal operations (e.g., landscaping, farming, or holiday businesses)
Cash flow issues or unexpected business expenses
Maternity/paternity leave for sole employee operations
Temporary layoffs or employee furloughs
Switching payroll providers
Whatever your reason, the key is to handle the pause correctly to remain compliant with labor and tax laws.
Here’s a step-by-step process to temporarily stop a payroll run:
Before doing anything, inform your team. Transparency reduces confusion and helps maintain trust.
If you're using Auto Payroll, follow these steps:
Go to Payroll > Employees
Click the Gear icon and select Payroll Settings
Under Auto Payroll, select Turn Off
Save your changes
This stops payroll from running automatically.
Navigate to Payroll > Overview
Under “Run Payroll,” skip the current cycle by not initiating a payroll run
You won’t be charged unless payroll is actually processed
Need help? Call +1-866-409-5111 for guidance on skipping payroll properly.
Open your company file in QuickBooks Desktop
Go to Employees > Payroll Center
In the “Pay Employees” tab, do not select employees for payroll processing
Close the window without clicking “Continue”
If you’ve set up a recurring payroll:
Go to Edit > Preferences > Payroll & Employees
Click Company Preferences
Under “Pay Schedules,” select the schedule and click Edit
Change the schedule date or temporarily remove it
While taking a payroll break might seem simple, avoid these mistakes:
Don’t delete employees from the system
Don’t cancel your payroll subscription unless you plan to stop payroll permanently
Don’t forget to file taxes or submit required zero-dollar filings if applicable
Don’t delay too long without notifying tax agencies
Here’s what to expect when you pause payroll:
No paychecks will be processed until you manually run payroll again
Benefits and deductions (like health insurance) may lapse
Tax filings still need attention—even if no wages are paid
To avoid compliance penalties, it’s wise to consult a QuickBooks payroll expert at +1-866-409-5111.
When you're ready to resume payroll:
Go back to your payroll dashboard
Re-enable Auto Payroll if needed
Re-run missed payrolls (if applicable)
Confirm employee payment info is up-to-date
QuickBooks makes it easy to restart when the time is right.
Knowing how to pause a payroll is just as important as running one. Whether it’s for strategic planning, financial caution, or just a business break—QuickBooks has the flexibility to adjust. Just make sure your method is legal, clear, and documented.