Integrating Payroll with HR Information Systems – why do mid-size organisations struggle?

Modern HR Information Systems and Payroll Systems support various integration protocols including direct API’s that are designed to ensure that the HRIS is the single-source-of-truth for employee pay & benefits and that this data flows seamlessly into the Payroll application to generate weekly, fortnightly or monthly payments to employees. Why then, do many organisations still have a myriad of spreadsheets to be completed and sent to the payroll team for each pay-run? 

Scale is a factor. Typically, these issues have been resolved at larger organisations with 3,000+ employees. At that scale, the dedicated technical and operational infrastructure is in place to maintain and support the automated dataflows and quality controls. But, for mid-sized organisations with 300 to 3,000 employees, preparing payroll data can be an additional task for someone who has another role in the HR or Finance department. Data quality can also be a factor with some examples as follows: 

  • Inadequate validation resulting is missing or transposed digits in bank account numbers 

  • New hires or Leaver’s status not updated in the HRIS 

  • Omission of some benefits from the HRIS (e.g. Pension contributions) 

  • Salary changes received via email after the cut-off time for payroll submission. 

Resolving the root-cause is the right thing to do, but that doesn’t happen overnight, so some pragmatism is required to get employees paid correctly in the meantime. To void spaghetti spreadsheet syndrome, here are a few practical suggestions to taming the payroll inputs: 

  • Leave the event-driven API until the technical resources are available to make it reliable.  Instead, implement a snapshot report from the HRIS to be generated for all employees on the cut-off day.  With less than 3,000 employees this is often a more manageable task than trying to sift through the valid and invalid time-stamped change events. 

  • Implement a structured Data Override process. Don’t be tempted to open and modify the HRIS data before it goes to payroll or send emails to change this or fix that. Create a structured table of overrides such as: 

Employee ID  Override Item  Override Value 
123456  A1001 : Monthly Salary €4,500.00
789012 B2005 : Employer Pension Contrib. 6% 


  • This will provide a structured audit trail, so everyone involved knows at a glance what needs to be done this month to get people paid. 

  • If you must re-work the data, try to avoid spreadsheets and use an ETL tool such as Microsoft Power Query, Knime or Alteryx.

After payroll is completed, write up a note of the root-cause of the issues that had to be addressed in the current month and circulate it to those with sufficient authority to implement the required change.