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Pay your employees in QuickBooks Online Standard Payroll

When you run a regular payroll in QuickBooks Online, you do 3 things:

  • create a payment
  • submit your real-time information (RTI) to HMRC (HM Revenue and Customs)
  • and then give employees their payslips


Running payroll for the first time in QuickBooks Online Standard Payroll?

Here's what you need to do if you're running payroll for the first time:

When you’re all set up to run payroll, you’ll see Complete next to Payroll Status and RTI Status.

Create the payment

  1. Go to the  Employees or Payroll menu, then select Payroll.
    Important: Make sure you've finished setting up all the employees you want to pay today. If an employee is missing some details and we need to create their payment or submit their RTI to HMRC, they won’t show up in the list when you run payroll.
  2. ​Select Run payroll.
  3. Make sure all of the employees you want to pay are listed.
    Note:  Select the slider next to a name if you want to remove the employee from this payroll.
  4. Double-check the pay date. If you want to change it, select the date and then choose another. Remember, the pay date must be within the pay period.
  5. ​Enter pay details for each employee.

    Add an earnings pay type (such as a bonus)

    If you don’t see all the pay types assigned to the employee, add the pay type in the employee profile. The pay type will be available to all the employees in your company, but you don't have to use it unless you enter an amount or percentage either in the employee profile or when you run payroll.

    • Any pay type that has a default amount will show up in the employee payment. For example, if an employee gets a  £100.00 monthly car allowance. You can edit the amount on the payment, but you’ll need to edit the employee profile if you want to change it for future payments.
    • Any pay types that are greyed out have been added in QuickBooks, but haven’t been assigned to the employee. Go to the employee’s profile to add a pay type.
    • If the employee is paid a salary, you’ll see the amount for the pay period. You can make changes, but the amount must be less than the regular salary.

    Add a deduction (such as a loan repayment)

    Add the deduction in the employee profile. Enter an amount or percentage in the employee profile. You can edit it when you run payroll.

    Check hourly pay for employees who are paid hourly

    If the employee is paid hourly, the default number of hours is set to 1. Enter the number of regular hours the employee worked during the pay period. Paying overtime? Add or customise other pay types in QuickBooks Online Standard Payroll (UK) .

    Check salary or hourly amount for part-time employees on statutory leave

    If the employee is part-time (that is, does not work a full week) and is on statutory leave, check the salary or hourly fields to make sure that this is calculated correctly. The statutory pay will be correct, but the salary or hourly pay might not be how you want to calculate it. Since there is no compliance requirement specifying the method of calculation, it is strongly recommended that you check the salary or hourly amount.

    Workplace Pension

    QuickBooks Standard Payroll supports payroll calculations and assessments for automatic enrolment. This means that the assessment is carried out when the payroll is processed. The PRP (Payroll Reference Periods) are based on tax periods. QuickBooks Standard Payroll does not support the alternate PRP method. The company staging date is always the 1st of the month. Because QuickBooks uses the tax period PRP, the assessment on the company staging date is carried out in the tax period during which the 1st of the month occurs.

    Example (monthly payroll): With a staging date of 1 May, the initial assessment is on the April payroll because the tax period is from 6 April to 5 May. When you run your April payroll, employees who are eligible to be automatically enrolled will be highlighted. You have the option to postpone or change their contribution.


    • An employee with another trigger after 5 May (for example, a person turning 22 during May) will not be included in the initial staging date assessment, but will be part of the ongoing assessment every payroll.
    • An employee with a mid-period trigger will be subject to the enrollment rules of the pension scheme you've chosen. If pro-rata pension is required, you will need to manually calculate and adjust the pension contribution accordingly. For example, an employee who turns 22 on 7 May could have to pay pension from this date or for the entire month.
  6. Select Save and review to see a summary of this payroll.
  7. If you want to review the payslip, select the amount shown in the Net Pay column (shown in blue text) to see a draft of the payslip. You can save the draft payslips to your device or print them out.
    See any problems? Go back and make any changes before you submit the payroll.
  8. Select Submit to create the payroll in QuickBooks.

What's next?

Next, you need to file the information with HMRC and give your employees their payslips.

  1. Submit FPS to HMRC in QuickBooks Online Standard Payroll (UK)
  2. Payslips in QuickBooks Online Standard Payroll (UK)

See also

Employees and payroll

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