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QuickBooks Online Payroll — Payroll Processing Instructions

1. Before Starting Payroll

[ ] Verify the pay period you are processing.

[ ] Verify the pay date.

[ ] Make sure all employee hours have been entered or approved.

[ ] Confirm any PTO, sick leave, vacation, holiday, overtime, bonuses, commissions, or reimbursements that need to be included.

[ ] Make sure new employees have been completely set up. [ ] Verify employee pay rates and deductions if there have been changes.

[ ] Make sure sufficient funds are available in the payroll bank account.

2. Open Payroll

1. Sign in to QuickBooks Online.


2. Go to All apps.


3. Select Payroll.


4. Select Employees.


5. Select Run payroll.


6. Select the appropriate pay schedule.


7. Select Continue

3. Verify the Payroll Dates

Review the:

• Pay period


• Pay date

Make sure these dates are correct before entering payroll. 

4. Select Employees

Select the employees who should be included in the payroll.

Review the employee list to make sure:

• Active employees who should receive a paycheck are included.


• Employees who should not be paid during this payroll are excluded.


• New or terminated employees are handled correctly. 

5. Enter Employee Pay

Enter or review the payroll information for each employee.

Depending on how the employee is paid, this may include:

• Regular hours


• Overtime hours


• Salary


• PTO


• Sick time


• Holiday pay


• Bonuses


• Commissions


• Reimbursements


• Other compensation 

To see additional information for an employee, select the appropriate payroll column or go to Actions → Edit paycheck.

If your company uses QuickBooks Time, select Review Approved Time and verify the imported hours. 

6. Preview Payroll

After entering everyone's pay information:

1. Select Preview payroll.


2. Review each employee's paycheck.

Check the following:

• Gross pay


• Employee taxes


• Employee deductions


• Employer taxes


• Other deductions or contributions


• Net pay 

Pay particular attention to employees whose paycheck is significantly higher or lower than normal. 

7. Verify the Payroll Bank Account

Confirm that the correct QuickBooks bank account is selected for payroll.

Make sure this is the account that should record the payroll transactions. 

8. Perform a Final Payroll Review

Before submitting, confirm:

[ ] Pay period is correct.

[ ] Pay date is correct. 

[ ] Employee hours are correct.

[ ] Overtime is correct.

[ ] PTO/sick/holiday hours are correct.

[ ] Bonuses and commissions are correct.

[ ] Gross wages appear reasonable.

[ ] Taxes appear reasonable.

[ ] Deductions and benefits are correct.

[ ] Net pay appears reasonable.

[ ] Correct bank account is selected.

[ ] Sufficient funds are available. 

9. Submit Payroll

When everything has been verified:

1. Select Preview payroll details if you want one final detailed review.


2. Select Submit payroll.


3. Wait for QuickBooks to confirm that payroll has been submitted.


4. Select Close when finished.

Important: Don't select Submit Payroll until you are satisfied that the payroll information is correct. 

10. After Submitting Payroll

After payroll has been processed:

[ ] Confirm payroll was successfully submitted.

[ ] Confirm direct-deposit employees are scheduled for payment.

[ ] Print paper checks for employees who receive physical checks.

[ ] Make pay stubs available to employees.

[ ] Review the payroll totals.

[ ] Save or review the appropriate payroll reports.

[ ] Verify that payroll liabilities and tax information were recorded correctly 

Processing an Unscheduled Payroll

Use an unscheduled payroll when you need to issue something outside the normal payroll cycle, such as a bonus or commission.

Go to: 

All apps → Payroll → Employees → Run payroll ▼ 

QuickBooks may provide options such as:

• Bonus only Commission only Fringe benefits only


• Select the appropriate option and follow the prompts.


• Review the payroll carefully before selecting Submit payroll.

Select the appropriate option and follow the prompts. Review the payroll carefully before selecting Submit payroll. 

Simple Payroll Workflow

Collect hours → Review hours → Open payroll → Enter pay → Preview payroll → Verify taxes/ deductions → Verify bank account → Submit payroll → Confirm processing → Review reports