Summary
Description
Once you install Sage 50 Payroll, you can set up your company and employee settings.
Enter your e-submission settings
So that you can submit directly to HMRC from your Sage 50 Payroll, you must enter your e-submission settings. These are the details you used to register with the online Government Gateway. More about e-Submission settings.
Set up departments and cost centres
If required, to help organise your employees, set up company departments and cost centres. You can create these in the Analysis tab within the company settings. Simply enter the department or cost centre reference and give it a name. Once you've finished, click Save. Then assign your employees to the relevant departments or cost centres when entering their information. Create and manage your Departments and Cost Centres.
Set up your payments and deductions
In Sage 50 Payroll, to pay your employees money or take any deductions, you need to set up payments and deductions.
Set up your pension schemes
If you have one or more company pension schemes, you need to set up a pension scheme in Sage 50 Payroll.
Set up your holiday schemes
If you have one or more holiday schemes for your company, you can enter this information into Sage 50 Payroll.
You can set up a specified entitlement holiday scheme or set up a calculated entitlement holiday scheme.
Enter your employee information
Once you enter your company level information, start entering your employee details and if required, their year to date (YTD) values. If you only have a few employees, you can enter their information manually using the Quick Employee wizard. However, if you have many employees, you can import their details into Sage 50 Payroll.
NOTE: Any employees who you've already made a leaver and submitted to Revenue don't need to transfer across. This means they aren't on any reports, so print off any reports you need for them from your previous software. Leavers don't affect your payroll at year end.
Enter your employees manually
Using the Quick Employee wizard, you can enter the relevant details for each of your employees in one window. All mandatory information has an asterisk (*).
Important considerations:
- RTI Payroll ID - Enter the employees' existing RTI ID from your old software provider. View our how to handle RTI IDs when changing software provider article
- Pensions - If you've already have an automatic enrolment scheme, assign any employees on the scheme to a pension scheme
When setting up the Pensions Module, confirm the auto enrolment status for these employees
Once you've entered the details for an employee, to save the details and clear the form ready for the next employee, click Save & Clear. Or to retain some of the basic details for the next employee, click Save & Retain. Read more on how to add an existing employee.
Import your details
If you have many employees, or have exported your employee information from your old software, you can import them into Sage 50 Payroll.
Once you have all of your employee information in the import template, to import the data you can use the Advanced Data Import wizard.
In the wizard, from the list of templates, ensure you select Employee Details and then browse to your template. Ensure you add the correct RTI ID to the template for each employee before you import data.
Enter your employees' YTD values

To ensure your employees tax and national insurance (NI) values continue to calculate correctly, you must enter their YTD values. You can find these on your P11 deduction reports from your previous software.
NI calculates using either the table method or the exact percentage method.
Sage 50 Payroll uses the table method. If you're comparing values to those calculated using the exact percentage method in your previous software, they’ll be slightly different. This is fine and accepted by HMRC. You can continue to process NI in Sage 50 Payroll using the table method.
To enter the YTD values for your employees manually, first select all employees.
You can then open Employee Year To Date Values, and enter the relevant values for the first employee. To move onto the next employee, click Save then Next. Repeat this process for each employee.
NOTE: Unless you edit your payslip layout, gross pay for NIC that you enter manually doesn't appear on employee payslips.
Check your data
Once you set up your company, there are a few extra things we recommend you do before you process your first pay period.
To ensure you've entered all the relevant information, you can use the useful Health Check option. It tells you if there are any issues that can cause your HMRC submissions to fail.
The Health Check option.
Employment allowance
First confirm with HMRC that you're eligible for employment allowance.
If you're eligible for employment allowance, set it up and submit a one-off employer payment summary (EPS), to let HMRC know.
Employment allowance and Apprenticeship levy
These are both impacted by mid-year setup and when entering YTD values. To ensure the values for are correct, either:
- Calculate the values manually, outside of the software, from the mid-year point
TIP: For help with calculating this outside of your software, go to Gov.UK.
- Or reprocess the payroll from the start of the tax year and the software will calculate these values automatically
Continue any statutory payments
If any of your employees are receiving statutory payments when changing your payroll software, set up the statutory payments to continue in Sage 50 Payroll. To do this, you need to process the remainder of the statutory payment manually. However, you can set up any new statutory payments to process automatically in Sage 50 Payroll. Visit the Statutory payments and holidays hub.
Statutory maternity, paternity and adoption pay
The following articles cover how to process these.
- Manual Statutory maternity pay (SMP)
- Manual statutory paternity pay (SPP)
- Manual Statutory adoption pay (SAP)
NOTE: If you submit an Employer Payment Summary to adjust your payment to HMRC due statutory parental payments, check the value is correct manually. Your software includes parental pay values you process, but this doesn't include values you processed with another software provider.
Statutory sick pay (SSP)
The SSP calculation is based on the gross pay an employee earns in the eight weeks before the period of sickness. However, when you move to Sage 50 Payroll, this eight weeks gross pay doesn't exist in the software.
An employee who meets the qualifying criteria gets SSP from the day they start with the company. To find out more visit the SSP eligibility and entitlement article.
If the employee's average pay is high enough to pay SSP, you can enter this information in their record. To do this, open the relevant employee's record, click Absence then SSP. Enter the AWE figure in the box to the right of the Auto Calc button then click OK.
If you've processed SSP in the eight weeks before you moved to Sage 50 Payroll, enter historical SSP to calculate linked periods of sickness.