Bi-annual Filing
Bi-annual tax filings are mandated by the South African Revenue Service (SARS) to ensure businesses maintain financial transparency and compliance.
Leveraging Agrigistics
Agrigistics streamlines the bi-annual filing process by providing automated checks, data validation, and final submission tools. Our system helps ensure employee and company data are accurate, reducing the likelihood of errors.
Bi-Annual Submission checklist
Clear all validation errors
How to clear employer detail errors
How to clear employee detail errors
In Bulk using the EPI sheet
On the individual employee
Ensure that you are in September or later before you can start filing
You have to have finalised all your periods in August before you will be able to generate the documents for filling.
So all your pay runs for the company needed to be finalised for August. Please see below guide that will show you how to finalise your pay run and to generate the documents for filing:
How to finalise a pay run How to generate documents for filing
Import Year to Date (YTD) figures - (if applicable)
Why would you potentially need to import YTD figures into the system?
If you migrated to our system during the financial year and you have processed periods for this financial year in a different payroll system you have the option to import the YTD's into our system so you don't have to import more than one IRP5 electronic file into e@syfile.
This is not mandatory - but is available to all clients to adjust to their preference.
What you need to import your YTD figures into our system is an excel sheet with these 3 columns:
Employee Code
Tax Total
Value linked to that tax total for the periods not processed in Agrigistics.
Please see below example of what your import sheet will need to look like:

How to import the YTD figures?
Navigate to Payroll, Filing.
Make sure that you are in the correct year, and in the correct company. It is ESSENTIAL that you select the correct company before continuing:

Click on Take-on Balances next to the date selection screen:

Locate the excel file that you have created with the import figures and click on OK.
Once the amounts have been processed, you won't get a message, however, the system will ask you to download the take-on-result file with the applicable year, this will show you if there where any errors and a summary of the information that has been imported.
Check for errors and download the IRP5 Validation report
Navigate to Payroll, Filing.
Make sure that you select the correct company on the left hand side.
Locate the August period, if there are errors that will not allow you to generate the file you will see that the IRP5 will say 'Can't generate until all errors are resolved' and there will be a red Error button on the right hand side of the August section:

When clicking on the Errors - it will give you a summary of any errors or warnings for this bi-annual season.

To see the full list of errors and warnings, you can click on IRP5 validation. This will download a zip file, double click on this file to open it. You will see the following reports in it:
Employee Pay Run List Report This will show you all the pay runs that the employees have been in that will assist with correcting any active period issues.
IRP5 Employee Personal Info This is an EPI sheet that will have all the employees that are part of the errors - and you can use this sheet to make corrections and import the details back into they system.
IRP5 Employee Totals This will show you all the tax totals and the values for those tax totals that will be on the electronic file for each employee.
IRP5 Validation Results This report will show you the list of all the errors, warnings and successes linked to this company
Open the IRP5 Validation Results excel sheet, all the items that shows as ERROR in the Severity column needs to be corrected. All the items that show as WARNING we advise that you check and ensure if the details are correct:

How to correct employer details errors
Steps to correct the company details:
Navigate to Payroll, Companies.
Locate the company and click on the pencil on the right hand side.
Edit the details that needs to be corrected and then click on save changes on the top right hand side.
How to correct employee details errors in bulk
Steps to correct the employee details:
Navigate to the zip file that you have downloaded for the IRP5 Validation and open the IRP5 Employee Personal Info document.
Click on Enable Editing right on top.
Now correct all the details for the errors on the IRP5 validation on this document.
In Excel, click on File, Save As and select a directory where to save this document to - you can change the name of the file if needed.
Now in the Agirgistics system, you will need to import these details:
Navigate to Payroll, Employees.
Click on Export/Import on the top right hand side.
Click on Import.
Select Import Personal Information.
Click on Import.
Locate the Excel sheet and select it, then click on Open.
Click on Upload file.
Click on Next.
Click on Validate.
If there are any errors - please correct the errors first. If there are warnings, or no errors you can click on Imports with warnings or import.
How to correct employee details errors per individual employee
Steps to follow to edit employee details per individual employee:
Navigate to Payroll, Employees.
Locate the employee in the list and click on their name and surname (not the check box).
Edit the employee details.
Click on Save changes.
Download the IRP5 Validation report again and ensure that all errors have been resolved.
Navigate back to Payroll, Filing.
Select the correct company on the left hand side.
Locate the August period and click on IRP5 Validation.
It will download a IRP Validation zip file.
Open the zip file and locate the IRP5 Validation report - make sure that there are no errors on the file. You can continue if there are warnings, but all errors needs to be corrected.
Generate the EMP 501
Navigate back to Payroll, Filing.
Select the correct company on the left hand side.
Locate the August period and click on EMP 501
Generate the IRP5 electronic file
Once all the errors have been resolved (the red error button on the left hand side has changed to a blue button) you will be able to generate the IRP5 file.
Navigate back to Payroll, Filing.
Select the correct company on the left hand side.
Locate the August period and click on IRP5
NOTE: This file will download a CSV file and the icon will look almost like a Excel file. This is the correct format for e@syfile. Do NOT open this file. Do NOT change the file type for this file.
Our file is based on the SARS Business Requirement Specification (BRS) document. There is only one version of this document active at any time and the requirements for import into e@syfile will be the same as importing into e-filing. We can only test the import into the e@syfile system, and due to this if the file imports into e@syfile and not into e-filing you will need to contact SARS.
The name of the file will be the company name, underscore, submission date, underscore, employer_recon: Company Name_20xx-08_employer_recon Below is screenshot of what the icon for the file will look like in different view types:

Import the file into e@syfile
Open up your e@syfile system.
Login using your e@syfile credentials.
Select your employer from the list and click on Continue.
Click on Import Payroll file
Click on Select File and locate the electronic file and click on Open.
Click on OK
The e@syfile system will now return the validation results, it will be one of the below options:
Payroll File passed Validation
Payroll File passed Validation with Warnings
Payroll File failed Validation.
After your file passed validation with or without warnings we can no longer assist you with e@syfile any further. If your file fails validation, please reach out to us for further assistance.
What is the Bi-Annual submission, and what terms do I need to look out for?
Employer Responsibility
While Agrigistics automates much of the process, the employer is ultimately responsible for ensuring the accuracy and timely submission of all data. Double-check entries, payments, and submissions to avoid discrepancies and penalties.
Key Submission Periods
• End of August: Consolidate data for the period from March to August
• End of February: Finalise the tax year by closing off data for the period from March to February
On the Agrigistics portal you will receive real time notifications for all bi-annual filing due dates:

EMP501
The Employer Reconciliation Declaration (EMP501) consolidates an employer's PAYE, UIF, and SDL obligations for all their employees during the tax year or bi-annual filing period. Essentially, it serves as a summary of all EMP201 submissions for that specific period, and, like the EMP201, includes information about the Employment Tax Incentive (ETI).
Tax Certificates (IRP5/IT3a)
Tax certificates serve as an official record of an employee's financial activities over a set period, capturing their income, deductions, and benefits.
Types of Certificates
IRP5s: Issued for employees with PAYE deductions.
IT3(a): For employees without PAYE deductions.
Issuing Certificates
It's mandatory for employers to provide these tax certificates to their employees. A printable tax certificate will only be generated by e@syfile in the case that a final certificate has been issued for an employee.
A final certificate is only issued either at year end, or when an employee is terminated prior to year end.
Tax Certificate Downloads and Validations
Agrigistics simplifies the EMP501 and IRP5 filing process through built-in health checks, validation tools, and a structured approach to final file downloads.

Filing Period Reports
In February and August of each financial year, you will have access to additional reports: EMP501 and IRP5
Error and Validation Checks - If there are any validation issues with your IRP5 or EMP501 documents, an error message will appear.
Click on the error to view a detailed list of issues that must be resolved before you can proceed.
File Download Restrictions - If errors are present during the filing period (February or August), you will not be able to download the EMP501 or IRP5 files. All validation issues must be resolved first.
IRP5 Validation Zip File - The IRP5 validation tool provides a ZIP file containing multiple Excel sheets. These files offer a detailed summary of all validation errors.
Error and Validation Checks
During a biannual filing period—either February or August—any outstanding errors or validation issues will prevent you from downloading your IRP5 or EMP501 files.

Click the Error button (Step 2: in the previous section) to view a full list of all issues identified during the validation process.
The system will display messages grouped into four categories:
Errors - will prevent you from downloading the tax certificates
Warnings - are not blocking, but it is good practice to address them where possible.
Information - are for reference only and require no action.
Success - confirm that the relevant sections are correctly completed—no further action is needed.
These critical errors must be resolved, and they are flagged in the validation file for review. For active period and tax code issues, manual intervention will be needed by contacting Agrigistics Support ([email protected]) will be required.
IRP5 Validation Zip File
After the validation checks, download the IRP5 Validation Zip File. This file provides a comprehensive summary of errors and warnings for you to review before final submission.
This file contains:
A detailed report of all critical errors and warnings.
A human-readable breakdown of the Employee Reconciliation File.
A filtered list of employees with outstanding information issues.
Carefully review this file and resolve any critical errors, such as missing employee information, active period or tax code discrepancies, before proceeding. Warnings do not require immediate action, but it’s important to be aware of them.
Reconciliation File Download
Agrigistics’ built-in validation tools minimise the chance of submission errors. If any unexpected issues arise, please contact support for assistance.
It is the client’s responsibility to inform Agrigistics about required take-on balances and ensure their timely submission. These balances are essential, as they directly influence the generated files.
Delays in submitting this information will result in errors or discrepancies during the reconciliation process.
Navigate to Payroll / Filing:

If the filing season is open and files need to be requested, you will see a notification banner at the top of the screen showing a countdown to the submission deadline.
Select the specific legal entity for which you want to download the reconciliation file.
Select the relevant financial year.
If the financial year has already ended, navigate back one year to download the filing documents for February.
Navigate to the correct filing month, either August or February.
If there are any errors present for the selected filing month, you will not be able to download the EMP501 or IRP5 documents.
Please refer to the Tax Certificate Downloads and Validations section above to resolve these issues before proceeding.
If there are no errors, you can proceed to download the IRP5 and EMP501 documents.
Once downloaded do NOT open this file as it can change the formatting of the file. To view the information in the file refer to the validation file that has been downloaded.
Helpful Tools and Resources for Filing
Embarking on the filing process can seem daunting, but with the right tools and resources, it becomes more manageable. Here's a selection of aids to facilitate your experience:
SARS Employer Guide
A comprehensive guide provided by SARS to navigate the e@syFile system. It offers step-by-step instructions, making the reconciliation and submission processes smoother.
Video Tutorial on EMP501 Submission
For those who prefer visual guidance, this video tutorial walks you through the EMP501 submission process, offering practical tips along the way.
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