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Centralising Payroll

Centralising payroll and consolidating multiple school PAYE schemes into a single Multi-Academy Trust (MAT) scheme reduces administrative overhead, improves reporting accuracy, and simplifies compliance.

However, moving multiple active payrolls into one central scheme requires meticulous planning across statutory bodies, pension administrators, and HR systems.

This actionable checklist covers every phase of centralising your MAT's payroll operations.



Planning & HMRC Alignment

Establish Scheme Consolidation Strategy

  • Decide whether to convert one existing school PAYE reference into the Trust Master PAYE scheme or register a new central reference with HMRC.
  • Set a clean migration date (ideally the start of the tax year, 6 April, to avoid mid-year RTI complications and duplicate P60 issuances).

Notify HMRC of Scheme Closures

  • Inform HMRC of the planned closure of individual school PAYE schemes.
  • Submit final Real Time Information (RTI) submissions (Full Payment Submissions and Employer Payment Summaries) marked as "Final Submission on Cease" for each outgoing school reference.

Nominate the Single Employment Allowance Claim

  • Confirm which central PAYE scheme will apply the single £10,500 Employment Allowance.
  • Ensure all outgoing school schemes cease claiming the allowance before the central scheme files its initial EPS.

Pension Scheme Re-alignment

Teachers’ Pension Scheme (TPS) Consolidation

  • Contact Teachers' Pensions to align all incoming schools under the MAT's central Employer Location Number (LEA/Estab reference).
  • Configure software for Monthly Contributions Reconciliation (MCR) reporting to ensure continuous automatic submission under the single master reference.

Local Government Pension Scheme (LGPS) Engagement

  • Engage with every relevant Local Authority Pension Fund (especially if the MAT crosses local council boundaries).
  • Confirm whether the administering authorities permit a single consolidated return or require sub-fund pool reporting by school location.
  • Update employer contribution rates for support staff across all sites according to the latest fund valuations.

Contractual & HR Data Integration

TUPE & Continuous Service Mapping

  • Audit terms and conditions across all schools (STPCD/Burgundy Book for teachers; NJC/Green Book for support staff).
  • Ensure all employee continuous service dates remain intact in the central database to prevent errors in occupational sick pay, maternity pay, and redundancy calculations.

Multi-Role & Split-Cost Standardisation

  • Map staff working across multiple academies (e.g., a premise manager covering three sites or a teacher working part-time at two academies).
  • Standardise cost center allocations so that single pay items are correctly split across individual academy budget codes.

Pay Scales & Allowances Reconciliation

  • Standardise pay spines across schools, including regional weighting differentials (e.g., Inner London, Outer London, Fringe, National).
  • Align claim-based pay items (overtime, supply cover, casual hours) onto a unified approval workflow.

Systems, Data Migration & Parallel Testing

Data Cleansing & Validation

  • Audit employee records: Review full records across legacy systems, including Tax codes, National Insurance numbers, Student Loan plan types, bank details, and pension categories.
  • Reconcile YTD figures: Ensure historic year-to-date figures are completely reconciled if migrating mid-tax year.

Parallel Payroll Runs

  • Traditional parallel payroll runs are not necessary when centralising with AcadaFix. Our built-in AcadaFix Smart Check automatically scans and highlights any errors or discrepancies in employee contracts directly during the onboarding process.
  • If you still prefer to run comparisons for peace of mind, AcadaFix strongly encourages testing against your historic payroll data rather than waiting to run a live parallel payroll. This allows you to validate the system immediately using your existing records, saving time and preventing delays to your implementation timeline.
  • Whether checking against historical data or a live run, keep the following in mind:
    • Legacy Inaccuracies: If records do not match, these variances are often the result of historical calculation inaccuracies in your previous payroll system.
    • Investigate Variances: When reviewing differences across gross pay, PAYE tax, employee/employer NI, TPS, LGPS, and voluntary deductions, take the legacy system's calculations with a pinch of salt before assuming an error in AcadaFix.

General Ledger & MIS Integration

  • Map systems: Link the centralised payroll software directly to your trust-wide finance and accounting software.
  • Verify journal exports: Ensure that exports accurately distribute payroll costs to each school's specific cost centre, department, and funder code.

Go-Live & Post-Migration Audit

First Central RTI Submission

  • Submit the first consolidated Full Payment Submission (FPS) under the master PAYE reference.
  • Confirm HMRC accepts the single starter details for migrated employees without generating duplicate tax records.

Employee Communication

  • Issue clear communications to all staff explaining changes to payslip appearance, tax reference numbers, and central payroll contact points.

Post-Migration Pension Audit

  • Perform a post-go-live reconciliation of the first MCR submission to Teachers' Pensions and LGPS schedules to confirm zero data errors or missing records.

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