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Managing employees in QuickBooks Online Advanced Payroll and Bureau Payroll

by Intuit•2• Updated 1 week ago

Learn how to manage employees in Advanced Payroll, including adding new employees, importing bulk data, managing qualifications, terminating employees, and handling payroll-related documentation.

This article is for customers who use QuickBooks Online Advanced Payroll and Bureau Payroll.


Adding an employee

Watch the quick video below to learn how to add a new employee to Advanced Payroll.

Before adding an employee, ensure you have their personal details (name, address, National Insurance number) and employment details (start date, job title, salary). Once you have this information, follow these steps:

  1. Go to Payroll and select the Employees tab.
  2. Select Add employee.
  1. Fill in the employee’s personal and contact details.
  2. Optionally, enable self-service so employees can access payslips and update details.
  3. Select Next.
  1. Enter the employee's start date, gender, and primary location.
  2. Choose a pay schedule and specify their pay rate (per annum, day, or hour).
  3. Define regular weekly work hours.
  4. If applicable, select Employee is paid irregularly. When reporting employees via RTI, you need to report how many hours they regularly work. This is done by using the following statuses:
    • A if less than 16 hours
    • B if 16 hours to 23.99 hours
    • C if 24 hours to 29.99 hours
    • D if 30 hours or more
    • E if you don't pay your employee regularly. Ticking this option will submit "E" on the employee FPS regardless of the number of hours they have worked.
  5. Assign the correct pay category.
  6. Select whether you are using a leave allowance template.
  7. Indicate if timesheets are used.
  8. Select Next.
  1. Choose an account type: Electronic (included in payment files), Manual (recorded but not processed electronically), or Cash/Cheque (no bank details recorded).
  2. Select Next.

Note: Pay runs are not paid automatically. It's your responsibility to pay the employees, either through manual payment or by downloading a payment file and uploading it to your internet banking provider.

  1. Provide the payroll ID if the employee has been previously reported to HMRC.
  2. Select whether IR35 rules apply.
  3. Enter the tax code.
    • If you're using a week one/month one code, tick box otherwise the code will default to cumulative. 
    • Don't include the X at the end of a tax code. For example, K325X should be entered as K325.
    • The X tells you to use the calculation method W1/M1.
    • The QuickBooks tax code notification feature automatically updates employee's tax codes without the need to manually the new tax code.
  4. If applicable, select whether the employee has student or postgrad loans.
  5. Enter the National Insurance number and NI category. If unknown, tick NIN unknown (NINO).
  6. If the employee is a company director, tick the relevant box.
  7. Select the employee type. If the employee is:
    • An existing employee, enter the opening balances.
    • A new starter, enter the employer PAYE reference, leaving date and total tax to date. You'll see an alert if the total tax to date stated does not match the total tax calculated. Select Check to compare the calculations.
      Note: P45 information will not transfer onto the current payslips for this employment.
  8. Select Next.

If you have enabled the 'IR35 contractors' option under HMRC settings, then the IR35 contractors option will be available for you to set, when creating employee records. You should have already used HMRC's Check Employment Status for Tax (CEST) tool, in order to find out the tax status of a new contractor:

IR35 Intermediaries legislation does not apply to this engagement

When you have completed the CEST check and this status has been returned, the software option chosen should be 'IR35 contractors' legislation does not apply', this contractor should continue to have their invoices paid in full, via the finance system.

IR35 Intermediaries legislation applies to this engagement

When you have completed the CEST check and this status has been returned, the software option chosen should be 'IR35 contractors' legislation applies', this contractor should have their invoices paid through your payroll, so that you can deduct tax and National Insurance from the work element of their pay.

  1. Choose the assessment method and enter the necessary details.
  2. Select Next to complete the setup.


Terminating an employee

When an employee leaves your business, you need to properly terminate them in QuickBooks Online Advanced Payroll. This process ensures they are marked inactive, their final payments are processed correctly, and they are excluded from future pay runs. You can terminate employees via their profile or during a pay run.

  1. Go to Payroll.
  2. Select the Employees tab.
  3. Open the employee's details page by selecting their name.
  4. Select Terminate Employee.
  5. Enter the Termination Date. This will mark the employee as inactive, making them ineligible for future pay runs and termination pay.
  6. Select Terminate.
  7. If you want to permanently delete an employee, select Delete employee.
    Important: Deleting an employee is a permanent action and cannot be undone. Once an employee is deleted, their data cannot be retrieved.
  8. Select Delete to confirm.

Note: You can't terminate an employee if they're included in pending pay runs.

  1. Go to Payroll.
  2. Select the Pay Runs tab.
  3. Open the pay run and select the employee.
  4. Select Actions, then Terminate employee.
  5. Enter the termination date and Save.

Once finalised, the employee will be inactive and removed from future pay runs. Any termination payments (leave payout, sick leave) will be calculated automatically.

  1. Go to Payroll.
  2. Select the Employees tab.
  3. Use the All Employees filter.
  4. Select the employee and click Re-Activate Employee. This will make the employee active again and eligible for pay runs.
  5. Confirm activation.


Importing employees in Bulk

Importing employees in bulk allows you to quickly set up multiple employees in Advanced Payroll. This is useful when migrating from another payroll system or performing a bulk update of employee details. To quickly add multiple employees, use the import feature.

  1. In QuickBooks, go to Payroll.
  2. Select the Employees tab.
  3. Select the ▼dropdown arrow next to Add employee.
  4. Select Export Employees.
  5. From the Data type dropdown, select Empty template.
  6. Choose whether you want to work with an XLSX or CSV file.
  7. Select Download.
  8. On your computer, open the template and add a row for each employee.
  9. When you're done, Save the file.
  1. Return to Payroll.
  2. Select the Employees tab.
  3. Select the ▼dropdown arrow next to Add employee.
  4. Select Import Employees.
  5. Select the file format, and then Select file....
  6. Confirm the upload.

To setup an employee to be processed in a pay run the following fields are required as a minimum:

  • First Name
  • Surname
  • DateOfBirth
  • ResidentialStreetAddress
  • ResidentialCity
  • ResidentialDistrict
  • ResidentialPostCode
  • PostalStreetAddress
  • PostalCity
  • PostalDistrict
  • PostalPostCode
  • StartDate
  • EmploymentType
  • PaySchedule
  • PrimaryPayCategory
  • PrimaryLocation
  • PaySlipNotificationType
  • Rate
  • RateUnit
  • HoursPerWeek
  • BankAccount1_SortCode
  • BankAccount1_AccountNumber
  • BankAccount1_AccountName
  • BankAccount1_AllocatedPercentage
  • NationalInsuranceNumber
  • NationalInsuranceCalculationMethod
  • NationalInsuranceCategory
  • TaxCalculationMethod
  • TaxCode
  • EmployeeStatement

Once an employee is set up in QuickBooks, import files may contain a smaller subset of fields but the following must always be included in order to be able to identify the employee to update:

  • First name
  • Surname
  • Date of birth

Fully qualified locations

Since locations may be nested when importing from the CSV file, it's important to specify the Fully Qualified Location. For the following set of locations:

  • All Offices
    • London Offices
      • Strathfield–the fully qualified location for ‘Strathfield’ would be All Offices/London Offices/Strathfield.
    • Devon Offices
      • Logan

If you're looking to remove data from employee records in bulk, you can do so by using an import file. Simply including the value clear in the appropriate field on your import file will remove the data from the matching field on the employee record.



Managing employee qualifications

Tracking employee qualifications ensures compliance and helps assign the right employees to the right tasks. QuickBooks allows you to store qualifications, set expiration alerts, and generate reports to manage workforce credentials efficiently. You can track employee qualifications and set alerts for expirations.

  1. Go to Payroll, and select the Payroll Settings tab.
  2. Select Qualifications under Pay Run Settings.
  3. Select Add.
  4. Enter the qualification name.
  5. Select Save.
  • Select the Bin icon next to the qualification.
  • If employees are linked to it, remove them first from their profile.

Running a qualification report is a great way to effectively identify which of your employees are linked to specific qualifications.

Note: QuickBooks will warn you if any qualifications that are currently expiring within the next 7 days.

To find out which employees are linked to qualifications:

  1. Go to Payroll, and then select the Reports tab.
  2. Under Employees, select Employee qualifications report.
  3. Select the date.
  4. Choose a qualification and status (Active, Qualified, Expired or Unqualified).
  5. Select Run report. You can Download the report in either a CSV, Excel or PDF file.


Employee self setup

The Employee Self Setup feature allows new employees to enter their personal details directly into QuickBooks, reducing admin workload and ensuring accuracy. Once the setup is complete, employers can review and finalise employee records for payroll. New employees can enter their details using Employee Self Setup.

  • To get started with the Employee Self Setup feature, the employer or payroll administrator will send an invitation to the employee.
  • This invitation will be sent to via email which will include a special link to access the setup wizard. 
  • The setup process consists of six steps that need to be completed in order to set up the employee's payroll information successfully.

The employee will be prompted to enter their personal information. Don't worry, some details may already be pre-filled based on the information provided during the initiation process. The required information includes:

  • Name, DOB, bank details, P45 details.
  • National Insurance number, tax code, emergency contacts.
  • Employees will need to review and submit their details.
  • After completing the setup, employers receive a notification and review the information before the employee is included in payroll.

By following these steps, you can efficiently manage your workforce in QuickBooks Online Advanced Payroll and QuickBooks Bureau Payroll.



Uploading employee documents

Advanced Payroll provides secure document storage for employee records, such as contracts and HR files.

  1. Go to Payroll, then Employees (Take me there). 
  2. Select your employee. 
  3. Select Documents. 
  4. If you want to upload to a folder, select the folder to open it. 
  5. Select Add documents ▼ then Upload from this device or Add from a mobile device. You can upload up to 10 MB per document.
  6. Follow the on-screen steps to select the documents you want to upload.
  1. Go to Payroll, and select Employees (Take me there).
  2. Select your employee.
  3. Select Documents.
  4. Select the document you want to share.
  5. Select Share from the Actions column.
  6. Confirm the document name and employee email. You can also add an optional message.
  7. Select Share.
  • Create folders: Go to Documents > Manage folders > Create folder.
  • Move or copy documents: Select a document > Actions > Move/Copy.
  • Download documents: Select a document > Actions > Download.
  • Delete documents: Select a document > Actions > Delete.

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