Current Pay Run

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New Features Update Announcement 14/03/2024

We're excited to announce several significant updates to our platform that are designed to streamline your payroll processes and enhance usability, especially on smaller screens.

  • Simplified Employee Addition to Pay Runs: Adding employees to a pay run has never been easier. Now, when you include new employees, the default earnings, deductions, and benefits will automatically apply, ensuring a smoother setup process.

  • Redesigned User Interface: We've overhauled our user interface to not only look better but also function more efficiently on smaller screens. This redesign focuses on accessibility and ease of use, making your experience as seamless as possible.

  • Enhanced Bulk Management Tools: Managing earnings, deductions, and benefits in bulk has received a major upgrade. Our new tools make it straightforward to see what has been added and simplify the process of making additions, saving you valuable time and effort.

These updates are part of our ongoing commitment to improving your experience and efficiency with our platform. We hope these changes will make managing payroll even easier for your business.

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, select the "Add Employee" option. 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

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.

To remove an employee from the current pay run:

  1. Choose the employee(s) from the table.

  2. A 'Bulk actions' option will become available once one or more employees are selected.

  3. Click on the bin icon to remove the selected employees.

Should you need to transfer employees between pay runs, they must first be removed from their current assignment.

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.

To manage an employee's pay run templates:

  1. Select the desired employees from in the table.

  2. Once you have selected one or more employees, a button labeled "Manage Templates" will become visible.

  3. Click on this button to begin adjusting the pay run templates for the selected employees.

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, 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: bonusses, hospital visits, shop purchases etc.

Add pay run templates

Follow the steps here to open the Manage Templates panel.

To add recurring templates to an employee's pay run:

  1. Click on the "Add Templates" button located within either the recurring or once-off sections.

  2. This action will prompt an additional side panel to appear, showcasing a list of all available earnings, deductions, and benefits.

  3. From this list, select the pay run templates you wish to apply and then click on the "Add" button to confirm your choices.

The selected pay run templates will then be applied to all employees you've chosen. Should any of the selected employees already have one of the templates you're adding, the existing template will be replaced by the newly added one.

Override pay run templates

Pay run templates can be overridden under specific conditions:

  • If the quantity of a pay run template is independent of clocking or piecework data.

  • If the rate of a pay run template is not determined by a variable.

Such templates are identified as Fixed Value Pay Run Templates, allowing for customisation of their quantity and rates. These adjustments can be made individually for each employee.

Follow the steps here to open the Manage Templates panel.

  1. Click on "Add Templates" within the recurring or once-off sections to initiate the template selection process.

  2. An additional side panel will display, listing all possible earnings, deductions, and benefits.

  3. As you browse the list, an "Override" option will become visible on fixed value pay run templates. Click on "Override" for the template you wish to adjust.

  4. Enter the new quantity and/or rate as required and select "Create Override". This action automatically adds the pay run template to your selection.

  5. Click on "Add" to apply the overridden template to all chosen employees.

Remove pay run templates

Follow the steps here to open the Manage Templates panel.

To remove recurring or once-off templates employee's pay run:

  1. Click on "Remove Templates" located in either the recurring or once-off sections. This action starts the template selection process.

  2. A side panel will appear, displaying all pay run templates currently applied to the selected employees.

  3. Choose one or more pay run templates that you wish to remove.

  4. Click on "Remove" to delete the selected templates from the chosen employees.

Import Fixed Rate Pay Run Templates

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.

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:

  1. Select Employees: In the table, choose one or more employees by selecting the checkboxes next to their names.

  2. Access Import Options: Click on "Import Pay Run Templates" button in the bulk actions section. Select "Import Earnings," "Import Deductions," or "Import Benefits".

  3. Select Pay Run Template: Choose the specific pay run template you want to import. Please note that only fixed rate pay run templates can be imported.

  4. Edit Rates and Quantities: On the following screen, you can edit the rates and/or quantities by clicking on the pencil icon (Option 1 in the photo) next to the respective employee's row.

    • Download Template (Option 2 in the photo): If desired, click on "Download Template" to download an Excel file. This file allows you to conveniently edit these values in an Excel format. You can also add more employee numbers to the Excel file if needed. If the employee in the sheet is not listed in the current pay run, you can remove them when uploading the file.

    • Upload Edited File (Option 3 in the photo): Once you've finished editing the Excel file, click on the "Upload File" button to repopulate the existing table with the updated values. Please make sure that the headers in the excel file is the same as in the downloaded template.

  5. Verify Information: Verify that the rates for each employee are correctly loaded. If needed click on the pencil icon next to the employee to change the value. If you want to remove the entire row, click on the trash icon.

  6. Assign as Once-off or Recurring: Finally, click on either "Once-off" or "Recurring" to specify whether the imported pay run templates should be added to all the employees as a one-time or recurring assignment.

By following these instructions, you can efficiently import pay run templates and tailor them to meet the specific needs of your employees.

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:

Employee Pay Run View

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.

  1. 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.

  2. Access More Options: Click on the "More" button, represented by three dots, located next to the "Add Pay Run Templates" buttons.

  3. Generate Payslips: From the dropdown menu, click on "Generate Payslips"

For a detailed breakdown on our payslips please follow the link below:



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.

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

  1. 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.

  2. 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.

  3. 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.

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.

PeriodEnd Date


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.


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.


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.

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:

  • 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.

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