Current Pay Run
View your latest pay run
Employee List
When you open a pay run, you will see a list of employees linked to the pay run. Each employee entry includes the following details:
Employee Name + Surname and Employee Number
Nett total - The total amount payable to the employee
Total Earnings
Total Deductions
Employee Notifications – Additional information related to the employee's pay run setup
Employee Search and Filters
You can filter by any notification tag using the filters at the top of the list.
Employee Template Notifications
Hover over any notification tag to view additional details.
Input Item Once-Off – The employee has a once-off pay run template.
Input Item Rate Changed – The rate for an input item has been overridden.
Input Item Quantity Changed – The quantity for an input item has been overridden.
Rate Value Override – A value system rate override has been configured for the employee. (Value overrides replace the existing system rate.)
Rate Factor Override – A factor system rate override has been configured for the employee. (Factor overrides are multiplied by the system rate.)
Default Config Missing – The pay run has no default configuration.
Default Config Items Missing – Not all pay run templates in the default configuration are assigned to the employee.
Default Config Extra Items – The employee has additional pay run templates beyond those specified in the default configuration.
Scheduled Rate – One or more system rates linked to the employee have a scheduled rate in the current pay run period.
Scheduled Rate Not Applied – The employee has an existing value override, which takes precedence over any scheduled rate.
Scheduled Rate Value Override – The scheduled rate for the employee has a value override.
Scheduled Rate Factor Override – The scheduled rate for the employee has a factor override.
Redundant Rate Value Override – The employee’s value override is the same as the system rate.
Loans & Savings - indicate specific events
Loan Payout
Loan Adjustment
Loan Settled - if the loan is repaid in full in the current period
Redundant Loan - the loan balance is R0 i.e. repaid in full
Saving Withdrawal
Saving Full Withdrawal - entire available balance will be paid out
Saving Adjustment
Add or Remove Employees from a Pay Run
Navigate to Payroll / Pay Runs and select the desired pay run.
Add one or more Employees
To add an employee to the current pay run:
Navigate to Payroll, Pay runs.
Enter the pay run you want the employee(s) to.
Click on the "Add Employee" button on the right.
Click on the plus next to the 'select employee' option and select the employee(s) from the list. NOTE: If the employee is not available for selection and in a peach colour then they are already in a different pay run and they need to be removed from that pay run before they can be added into the new pay run. NOTE: If the employee is not in the list, please make sure that they have been added to the Manage, Employee screen. If they are please refresh the page and add them again.
The link recurring template section will show you all the templates already linked to the pay run. You can use the pencil to add templates (it will link those templates to all the employees you have selected) or you can remove templates if they don't need to be on these employees (it will remove it from the employees selected).
Once you are happy with your selection you can click on Add.
Please click on the green circle to go through a simulation of this:
This action will link the chosen employee(s) to the current pay run. It is essential to understand that added employees are automatically added as recurring. Therefore, upon finalisation of the current pay run, these individuals will be included in subsequent pay run as well.
Once employees are selected, they will automatically inherit the default pay run template configuration. Should you wish to modify the templates for the selected employees, you can do so at this stage. Please note, altering pay run templates for individual employees during this process does not affect the default configuration of the pay run. To adjust the pay run's default settings, click here.
When adding employees, you'll notice that employees who are already associated with other pay runs are marked in red and employees already linked to the current pay run is gray. If you intend to include an employee of another pay run, you must first remove them from their current pay run.
Remove one or more Employees
To remove an employee from the current pay run:
Navigate to Payroll, Pay runs.
Enter the pay run that the employee is in.
Choose the employee(s) from by clicking the check box.
A formerly hidden 'Bulk actions menu' option will become available once one or more employees are selected.
Click on the trash can icon to remove the selected employees.
If you want to add this employee to a new pay run with the same PAYE number we advise that you refresh the screen before adding them into the other pay run.
Please click on the green circle to go through a simulation of this:
Removing employees from a pay run affects only their current, unfinalised pay run, preserving their historical pay run records. Thus, when examining the history of this pay run, previously removed employees will still appear.
Should you need to transfer employees between pay runs, they must first be removed from their current pay run - our guide can be found here.
If you are moving an employee from a pay run linked to Company A (with PAYE number 71234568) and they need to move to a pay run linked to Company B (with PAYE number 78901234) it is important that we terminate the employee first, then enroll them when they move into Company B's pay run - we also need to make sure to give them a new start date - our guide can be found here.
Employee Overview Shortcut
Navigate to Payroll / Pay Runs and select the desired pay run.
All the employees in the current pay run is linked to live data on the Employee Overview Report. All clocked hours and activities that are associated with pay run templates will update as soon as the information is captured.
Information from the Employee Overview Report is only linked to the employees if they are configured in the Pay Run Templates.
Click on the "Employee overview report" button to navigate to the overview report with all the employees in the current pay run and pay run period already selected.
Manage Pay Run Templates
After adding employees to the current pay run, the default configuration will automatically apply. Beyond this default setup, you have the flexibility to add or remove pay run templates for individual employees as needed. Please refer to this section for guidance on creating and adjusting your pay run templates.
Each pay run template can be assigned to an employee only once, which means duplicates of a single pay run template are not possible.
Manage pay run templates should be used to either Remove templates from an employee, or Add templates that are linked to the EOR to employees. You can do this by navigating to:
Payroll, Pay runs.
Enter the pay run you want to add or remove templates from.
Select the desired employees from the list by clicking their checkboxes
A formerly hidden 'Bulk actions menu' option will become available once one or more employees are selected.
Click on Manage pay run templates.
A side panel will appear, you can either click on Add templates or the plus icon in either the recurring templates OR the once off templates section Read below for more details on when to select which option
Click the checkbox for the templates you want to add.
Click on Add
You can now close the side panel.
After clicking on "Manage Templates" a side panel will open, presenting two sections that list all the existing pay run templates associated with the selected employees. This layout offers a comprehensive overview of the templates currently applied to all chosen employees. Within this side panel, you will have the ability to add or remove both recurring and once-off pay run templates.
Recurring or Once-off
Pay run templates can be added in one of two ways: recurring or once-off. When selecting "recurring," the pay run template will automatically be applied to the same employee for the next pay run once the current one is finalised. However, if it is added as a "once-off", it will not appear in the next pay run once the current one is finalised.
Recurring templates are used for earnings and deduction that are always present on the employees pay run eg. Normal Hours, Fixed Salary, Overtime, Housing Deduction etc.
Once-off templates are earnings and deductions that are only applicable to a single pay run or when their values differ each pay run. Examples of these are: bonus, hospital visits, shop purchases etc.
Manage Pay Run Template vs Import Pay Run Templates
The Manage Pay Run Templates feature is ideal for applying templates to employees when the template details are uniform across multiple employees.
It is the only way to remove templates.
Suitable for templates where values are identical for each employee or depend on the Employee Overview Report.
The Import Pay Run Templates feature is best for situations where the template is applied to multiple employees, but the amounts vary per person. This method allows you to load individualized values for each employee efficiently.
Examples of templates to add via Import Pay Run Templates:
Shop deductions
Electricity charges where different employees use varying units
Ad hoc bonuses
Reimbursements
Remove pay run templates
You can do this by navigating to:
Payroll, Pay runs.
Enter the pay run you want to add or remove templates from.
Select the desired employees from the list by clicking their checkboxes
A formerly hidden 'Bulk actions menu' option will become available once one or more employees are selected.
Click on Manage pay run templates.
A side panel will appear, you can click on Remove Templates in either the recurring templates OR the once off templates section
Click the checkbox for the templates you want to remove.
Click on remove.
You can now close the side panel.
You can click on the green cursor below to click through a visual representation.
Add Adhoc templates to employees.
When you need to add the same fixed-rate template for multiple people with varying values, you can import them in bulk.
Pay run templates that are imported must be configured as fixed values; the quantity cannot be linked to clocked hours or piecework data and the rate cannot be linked to a system rate.
Here are a couple of examples of when you might want to import values for a pay run template:
Shop Deductions: If you need to deduct employee purchases at the end of each pay period, and each employee spends a different amount.
Electricity Purchases: When employees can purchase multiple tokens per month, and the quantities differ among individuals.
To import these values, follow these steps:
Navigate to Payroll, Pay Runs.
Enter the pay run you want to add or remove templates from.
Select the desired employees from the list by clicking their checkboxes or select the select all checkbox if it applicable to all employees
A formerly hidden 'Bulk actions menu' option will become available once one or more employees are selected.
Click on Import Pay run templates.
Select the type of template that you want to Add (you can only add one template at a time)
From the drop down, select the template you wish to add from the list.
Click on Next.
You can now manually add in the amounts and/or quantities and rates for the employees. Remember: you can copy and paste amounts if needed - or set a uniform amount for all employees by clicking on Manage, Set uniform amount.
Once the amounts have been added you can either select to add the template as:
Once off - this template with this amount will only be on the current period and will be removed from the payslip once this pay run has been finalised. Examples: Shop Purchases, Breakages, Bonus, Reimbursives, Electricity units used, Commission etc.
Recurring - this template will stay on these employees payslips after this period has been finalised and the amount will stay as is until you either manually remove the template or override the amount. Examples: Garnishee orders, Travel Allowances, Medical Aid, Retirement Annuities etc.
Once you have selected which option is applicable, you will get a successfully updated panel that you can close
Importing ad-hoc templates via Excel
You can use our template for the Excel sheet or generate your own. To download our template: Go to Payroll, pay runs. Click on pay run you want to add the templates to, click on the select all checkbox. Click on Import Pay run templates. Click on the type of template you want to add. Click on the drop down and select the template. Click on Next. Click on manage. Click on Download.
It is important to note that you can import any excel sheet into our system. However, the sheet will have to have a column with the below and the column needs to have a heading:
Employee code - In this column the employee codes as they appear on our system has to be present
Amount and/or quantity - depending on the type of template you are importing it might just be a once off amount or it might be a template that has a quantity and a rate.
You can have multiple columns with different templates and and amounts linked - but you will have to import the sheet multiple times because you can only import one template at a time.
Please make sure that the sheet is free from calculations - you can copy the calculations and paste them as values in excel in order to do this
Navigate to Payroll, Pay Runs.
Enter the pay run you want to add or remove templates from.
Select the desired employees from the list by clicking their checkboxes or select the select all checkbox if it applicable to all employees
A formerly hidden 'Bulk actions menu' option will become available once one or more employees are selected.
Click on Import Pay run templates.
Select the type of template that you want to Add (you can only add one template at a time)
From the drop down, select the template you wish to add from the list.
Click on Next.
Now click on Manage
Click on Upload.
Locate the directory where your Excel file is saved and click on it - then click on Open.
The system will ask you to Map your excel sheet:
In the employee number sheet click on the drop down and select the heading of the column where your employee number is located.
In the Rate click on the drop down and select the heading of column where the amount for this template is
Click on update
Now scan through the amounts that has been imported, if happy you can add it to the system by selecting either:
Once off - this template with this amount will only be on the current period and will be removed from the payslip once this pay run has been finalised. Examples: Shop Purchases, Breakages, Bonus, Reimbursives, Electricity units used, Commission etc.
Recurring - this template will stay on these employees payslips after this period has been finalised and the amount will stay as is until you either manually remove the template or override the amount. Examples: Garnishee orders, Travel Allowances, Medical Aid, Retirement Annuities etc.
Once you have selected which option is applicable, you will get a successfully updated panel that you can close.
Employee View
Click on an employee in the table to view detailed list of all pay run templates. Refer to this section for more information on the following:
Override system rates
Add and modify active periods
View and edit leave balances
Generate Payslips
A payslip can be generated for a single employee or the entire pay run. To generate payslips from the pay run view please follow these steps.
Please make sure employee and employer information is configured correctly to make sure that all the legally required information is present on each pay slip.
If the filing details under the employer information is not configured, it will not be displayed on the payslips.
Generate Multiple Payslips
Navigate to Payroll / Pay Runs and select the desired pay run.
Select Employees: In the table, choose one or more employees by selecting their checkboxes. Click on the top most selection box to select all the employees in the pay run.
Access More Options: Click on the "More" button, represented by three dots, located next to the "Add Pay Run Templates" buttons.
Generate Payslips: From the dropdown menu, click on "Generate Payslips"
For a detailed breakdown on our payslips please follow the link below:
PayslipWhatsApp Current Payslips
This feature allows you to notify employees in a specific pay run that their payslips are ready to be viewed on WhatsApp.
By default, employees cannot access their current payslips for a new or rolled-over pay run. This restriction prevents them from viewing payslip information before the pay period is finalised. You must first grant access and then send a notification before employees can request their payslips.
If you prefer employees to see their earnings accumulate during the pay period, you can grant them access earlier. However, the standard process is to enable access and notify them only when the payslips are final.
Step 1: Granting Payslip Access for the Pay Run
First, you need to enable access for all employees within the pay run. This action allows employees to request their payslips via WhatsApp but does not send them a notification.
Navigate to the pay run.
In the Overview panel on the left, locate the "Payslip access via WhatsApp" section.
Click on the button that says "None" and select "Give all access" from the dropdown menu.
Once this is set, all authenticated employees in this pay run will be able to request their payslip from WhatsApp.
Step 2: Notifying Employees that payslips are ready
After granting access, you can send a notification to inform employees that their payslips are available.
In the pay run, select the employee or employees you wish to notify.
You can select all employees by ticking the checkbox at the top of the list.
Click on the Manage Payslips button in the action bar.
From the dropdown menu, select Notify WhatsApp payslips are available.
A confirmation window will appear, showing a list of employees who were successfully notified and a separate list of any unsuccessful notifications. Each unsuccessful attempt will include a reason why the message could not be sent.
The Employee Experience
Employees will receive a WhatsApp message notifying them that their latest payslip is ready. When they request and download the payslip, it will be a password-protected PDF.
To open the document, they will need:
A PDF viewer application installed on their mobile phone.
Their South African ID number or Passport number to use as the password.
Pay run Reports
Navigate to Payroll / Pay Runs and select the desired pay run. Click on the reports tab to view pay run specific reports.
Cost report: Provides a detailed breakdown of all earnings and deductions for each employee, offering a comprehensive view of payroll expenses.
Nett pay report: Combines each employee's net pay with their banking information. This report is particularly useful when generating payment files that are not currently supported by the system.
Bank payment files: To perform batch actions with your bank, you can download a bank-specific file. For guidance on exporting the correct file for your bank, please refer to the information provided on this page.
Cost report
Navigate to Payroll, Pay runs.
Enter the appropriate pay run.
Click on Reports.
Click on Export next to Cost Report (New):
Nett pay report
Do NOT generate the Nett pay report if you have not as yet generated the payslips or the cost report.
Navigate to Payroll, Pay runs.
Enter the appropriate pay run.
Click on Reports.
Click on Export next to Nett pay report:
Bank Payments
At Agrigistics, we recommend the following process for bank payments:
EFT payments to employees cannot be initiated if any of the following information is missing:
Employee payment method (EFT) and banking details
Employer banking details
Payslip Distribution: We suggest printing payslips and distributing them to employees before initiating a bank payment. This step allows you to make any necessary adjustments to payslips if errors or missing information are identified.
Verification by Employees: Once the employees receive their payslips, they can review them to ensure accuracy. If there are any discrepancies or concerns, this provides an opportunity for resolution.
Generate Bank Payment File: Only after employees are satisfied with their payslips, proceed to generate the bank payment file. This step ensures that the payment data is accurate and error-free before the funds are transferred to employees' bank accounts.
For more information on bank exports that we provide: Bank Payments.
Edit Start and End Dates
It is possible to change the start and end dates of a pay run given the following circumstances:
You can only adjust the start and end dates of a pay run, not the period itself. This means if you have set up the pay run on a Monthly or Weekly basis, you may only alter the end date provided it does not impact the period.
Edit Start Date
This is only possible if there are no previous finalised pay runs within a recurring pay run. When beginning the onboarding process, you can modify the start date of your first pay run to any date you prefer. This method allows for conducting multiple trial runs in succession without finalising incorrect information.
How to change the start date:
Navigate to Payroll, Pay runs.
Go into the pay run that you want to change.
You will see the date for the pay run on the right hand side more to the top.
Click on the pencil next to the date.
Click on the start date block and use the calendar to select the correct date (Please do NOT try and edit the END date along with the start date - the system will then only change the end date).
Click on Confirm.
Refresh the web page for the views to update.
Changing the start or the end date will adjust the duration of this pay run and it can change the calculated figures for: Leave accrual Leave Pay out Hours/overtime hours worked
Edit End Date
You may edit the end date of a pay run at any time, provided it does not impact the period. The following table summarises the ways in which you can adjust the end dates of a pay run:
By shortening the duration of a pay run, you will automatically increase the duration of the next period.
Monthly
There can only be one pay run in a calendar month. If a monthly pay run starts after the first day in a month, it must end in the next calendar month.
Fortnightly
There can only be one pay run every two weeks. If a fortnightly pay run starts on a Tuesday, it must end within the calendar week two weeks after the Tuesday.
Weekly
There can only be one pay run every week. If a weekly pay run starts on a Tuesday, it must end in the next calendar week.
How to change the end date for a pay run:
Navigate to Payroll, Pay runs.
Go into the pay run that you want to change.
You will see the date for the pay run on the right hand side more to the top.
Click on the pencil next to the date.
Select End date (if the pay run has been finalised before, Start date will be greyed out).
Click on the start date block and use the calendar to select the correct date.
Click on Confirm.
Refresh the web page for the views to update.
Changing the start or the end date will adjust the duration of this pay run and it can change the calculated figures for: Leave accrual Leave Pay out Hours/overtime hours worked
Finalise a pay run
Finalising a pay run in Agrigistics ensures data integrity, accuracy, and compliance with statutory requirements. The following section outlines the key steps and considerations for this process.
When do I finalise?
Finalising a pay run, as the term suggests, is irreversible. Once a pay run is finalised, no changes can be made to any information associated with that pay run. Before finalising, please consider the following:
SARS Filing: After finalisation, the pay run will automatically be included in the filing process, which encompasses both monthly and bi-annual submissions. Any inaccuracies within a pay run will be reported to SARS. Finalising an incorrect pay run can lead to reconciliation issues and potentially result in fines.
Ensure the amounts paid to each employee match exactly what is stated on their payslips.
Verify that all statutory deductions are accurate and accounted for. For guidance on enabling UIF and PAYE, click here for more details.
During the onboarding process, if you wish to roll over the current pay run without finalising it, please click here for further instructions.
Periods: Once the end date of a pay run is changed, it cannot be modified post-finalisation.
Should you need to adjust the end date of a pay run, refer to this section for detailed information.
Exercise caution when changing the end dates of pay runs. For additional insights, click here:: Why only Monthly, Fortnightly or Weekly?
It is of extreme importance to maintain the integrity of a finalised pay run. Finalised pay runs must be an exact replica of what was printed and distributed to each employee. This practice ensures that the employer can consistently verify the accuracy of their information, thus preventing any allegations of post-pay slip alterations by employees.
Finalised pay runs also play a crucial role in the generation of reconciliation reports for the South African Revenue Service (SARS). Any alterations to this information can result in discrepancies and may lead to regulatory fines.
Pay runs can only be finalised after the period has concluded. This ensures that any live clocking data can still be allocated to the correct employees. When finalising a pay run, it will automatically generate a new pay run with the same period starting the day after the previous pay run has ended.
To finalise a pay run, navigate to Pay Runs and select the desired pay run. In the top right hand corner click on the "Finalise pay run" button.
If the Finalise pay run button is greyed out, it means that this pay run is not yet ready to finalise. You can only finalise a pay run after the end date.
In conclusion, at Agrigistics, we recommend finalising the pay run only after payslips have been distributed and payments have been made. This approach allows for any necessary corrections to be made before finalising, preventing the submission of incorrect information.
Verify your data before finalisation
Before finalisation, thoroughly review the following elements to ensure correctness:
To prevent accidental finalisation of the incorrect pay run, a 24-hour cooldown period applies before you can finalise another pay run within the same Recurring Pay Run. This ensures sufficient time to review and confirm that the pay run is correct before finalising. Our support team can bypass this restriction in the event where multiple periods must be finalised at once.
Time & Attendance Data data:
Verify that all time and attendance data for each employee is accurate and correspond to their clocking templates.
Confirm that all piece work and activity records are correct and configured with the correct rates.
Resigned employees:
Employees that are scheduled to be resigned in the current pay run will be removed automatically once you finalise.
Leave Records:
Ensure all leave is correctly captured and updated.
Statutory deductions:
Review and verify statutory deductions for compliance. Make sure that all applicable employees are enabled for UIF and PAYE.
A finalised pay run should represent an accurate and unchangeable record. Any changes to piece work data, time and attendance hours, or other details will not impact the finalised pay run. This is crucial to maintain data integrity and ensure that any changes to the underlying data have no affect on your payroll data.
Pay Runs History
After finalising a pay run, a new pay run for the subsequent period is automatically generated. All finalised pay runs are accessible under the Pay Run History tab.
To view, navigate to Pay Runs and select the pay run of interest. Open the Pay Run History tab to see all finalised pay runs.
This section allows you to view all finalised pay runs and the dates they were finalised. By clicking on the pencil icon next to a finalised pay run, you can view its details and generate any required reports or payslips.
Please be aware that once a pay run is finalised, it is not possible to add or remove any employees or alter their pay run templates.
Archive a Pay Run
Archiving a pay run is a critical step in managing the payroll process, especially after completing a season or project involving temporary workers. Here’s a detailed guide on how to archive a pay run, ensuring that all necessary steps are followed and that your payroll data remains intact and accessible for future reference.
When to Archive a Pay Run
All temporary workers’ contracts have ended, and they have been resigned with their leave paid out. As soon as their last pay run is finalised they will be automatically removed from the next pay run.
Once the pay run is empty, i.e. there are no more employees on the pay run, the system will prompt you with a screen indicating that you can now archive the pay run.
You must archive a pay run before you can generate the monthly EMP201 reports. Even if a pay run is empty, the monthly reports will not be generated until it is archived. This is to prevent employees from not being included in the monthly reports.
It is important to consider the following before archiving a pay run:
Accessing Historical Data: Even after a pay run is archived, you can always go back to access historical data. This ensures that you can generate payslips for individual employees as needed. For more information on reports that can be generated for employees refer to this section: Payroll Reports.
Irreversible Action: Once a pay run is archived, it cannot be activated again. If you need to manage payroll for a new season or project, you will need to create a new pay run with a new start date.
Properly archiving pay runs ensures that there are no gaps between the last pay run and any new pay run that might start in a subsequent season or for a new project.
Compliance: Always make sure to resign all employees officially before removing them from a pay run to comply with employment laws and payroll regulations.
By following these steps, you can effectively manage the end of season or project payroll responsibilities, keeping your records organised and ensuring compliance with all necessary procedures.
Last updated
Was this helpful?