When your business experiences structural changes — like mergers, acquisitions, or ownership transfers—it’s crucial to reassess how you manage payroll. These changes can substantially impact how employees are paid, taxes are computed, and which PAYE reference numbers apply. Mismanagement of this procedure can result in compliance issues, payroll delays, and problems with HMRC. Payroll management must be a major priority in any corporate change. Whether you’re executing a merger, succession, or part-scheme transfer, you’ll need a clear plan to keep your payroll running efficiently and lawfully.
In this guide, we’ll walk you through the key steps involved in adjusting your payroll process during business changes. This article covers all you need to know about remaining in complete compliance with HMRC laws, from establishing the relevant employer references to filing accurate payroll reports.
Mergers & Successions
Business expansion is frequently associated with complexity. Payroll migrations following mergers and acquisitions are one example of such complexity. If your company combines with another or is bought by a new legal entity, you may need to update the employer reference for payroll management. These situations are classified into two categories: mergers and successions.
What’s the difference?
- A merger is often the integration of two or more PAYE schemes under a single business structure.
- A succession, on the other hand, occurs when a different legal entity takes control of your business and becomes responsible for employee pay records. This commonly occurs during business transactions, liquidations, or administrations.
In either scenario, you should start by contacting the HMRC Employer Helpline. They will confirm whether your situation qualifies as a merger or succession. Based on their assessment, HMRC will:
- Tell you which employer reference to continue using
- Provide a new employer reference if necessary
- Offer guidance on how to transition your payroll records properly
Staying abreast of these changes is critical. Proper payroll management during mergers and successions allows you to avoid errors, late submissions, and penalties.

Moving Employees to a New Payroll
Moving employees from one payroll arrangement to another requires careful consideration. How you manage this is determined on whether the payroll remains under the same employer reference or is transferred to a different one. This stage is especially crucial in mergers and acquisitions payroll migrations, which may involve many employer references.
Moving Under The Same Employer Reference
If you’re merely restructuring payroll while keeping the same employer reference, your strategy is clear. Continue to report payroll data using the existing PAYE reference. Keep personnel records uniform and accurate within your software.
Moving To A Different Employer Reference
If you’re transferring employees to a new payroll with a different employer reference, the process becomes more detailed:
- Submit a Final FPS under the old employer reference: Include all leaving details for each transferring employee. Keep precise records of their year-to-date salary and tax information.
- Do not issue P45s: Instead, give employees a document showing total earnings and deductions up to the point of transfer.
- Submit a new FPS under the new employer reference: This FPS should contain their updated payroll information and start dates.
- Update your payroll system: Ensure that all employee data reflects the new PAYE configuration and meets reporting standards.
Effective payroll management during this time ensures continuity and compliance with HMRC’s objectives. Proper transitioning preserves employees’ tax records and national insurance contributions.
Submitting Full Payment Submissions (FPS)
A key part of payroll management during any business change is knowing how and when to file Full Payment Submissions (FPS). This report tells HMRC how much each employee earned and what deductions were made. If your company is transitioning to a new PAYE reference, here’s how to prepare your first FPS appropriately.
Starting Fresh with New Reference
For the first FPS under your new employer reference:
- Restart year-to-date figures at zero: Under the new payroll system, all employee totals are reset.
- Include complete starter information: This means start dates, tax codes, and relevant starter declarations.
- Use the correct starter declaration: Starter declaration C is used for Business Reference (BR) codes or codes that begin with “D”. All other tax codes should be entered using beginning declaration B.
These details ensure HMRC can match employee records and tax contributions properly. Submitting an accurate FPS also helps to avoid confusion in tax coding and keeps payroll procedures running smoothly.
Finally, always submit your final FPS using the old reference before submitting your first with the new one. This maintains a clean record for HMRC and ensures a smooth transition in your payroll data. Good payroll management techniques necessitate precision, especially when your organization is evolving. Whether you’re adjusting to a merger, managing a succession, or migrating workers, timely and accurate FPS filings are critical.

What to Do on Your Payroll
Changing your payroll systems becomes a first concern when your company experiences structural changes including a merger, acquisition, or succession. Good payroll control guarantees compliance, helps to prevent fines, and guarantees accurate and timely payment of your staff.
Deduct Correct Contributions
First, after employees move to a new payroll, make sure you are taking the right amounts from their pay. You still have to apply:
- Pay As You Earn tax
- National insurance contributions
These reductions apply whether your company runs under a new or the same employment reference. Preventing anomalies and guaranteeing a seamless transfer depend on constant and clear payroll management.
Recognise Tax Code Repercussions
Then, if you use a cumulative tax code, go back to the pay and tax information of the previous payroll. Preventing mistakes in year-to-date computations depends on this stage. Conversely, for non-cumulative codes, zero year-to-date values are required when configuring the new payroll system.

Communicate With Staff
Keep your staff updated also during the change. Employees nevertheless need a thorough analysis of their salary and deductions up to the time of transfer, even though a P45 is not required during a transfer under different employer references. Open payroll systems help to lower uncertainty and foster trust.
Promptly Update Internal Payroll Systems
Be sure to:
- Record new start dates of staff members.
- Use the proper tax codes and first declarations.
- Only reset year-to-date amounts when needed.
This part of the payroll procedure for businesses demands accuracy. Errors here can compromise employee morale, pension contributions, and tax obligations. Most importantly, good payroll management protects your employees and ensures business continuity, especially during complex mergers and acquisitions, and payroll transitions.
Submitting P11D Forms
Accurate reporting of employee benefits is yet another important chore during business transitions. P11D forms come in handy here. The kind and quantity of P11D paperwork you have to turn in depend on how your payroll system is now set up.
During a PAYE Scheme Merger
Should your organization have consolidated its PAYE systems, you must send two P11D forms for every employee receiving company benefits:
- Up until the merger date, one under the original PAYE reference.
- One after the merger date under the new PAYE reference.
However, if the business underwent a merger without consolidating PAYE schemes, only one P11D form per employee is required.

During a Business Succession
For successions reported to HMRC already, the procedure is easier. You should send a single P11D form under the new employer reference. This form should cover the whole reporting period including advantages from the old and new PAYE systems.
Should you not have told HMRC of the succession, you have to send two P11D forms:
- Under the former reference, up to the succession date
- One under the new reference, from that date forward
In either case, accurate payroll management is crucial to ensure correct reporting and avoid costly penalties.
For a Part Scheme Transfer
In a part scheme transfer, submit two P11D forms per affected employee:
- Under the old employer reference, up until the transfer date
- From the transfer date forward, one will be under the new employer reference.
Strong documentation and organized payroll management will help you navigate these situations smoothly, especially in the context of mergers and acquisitions payroll.
Conclusion
Mergers, acquisitions, and successions present administrative issues. An efficient and compliant payroll system is essential. Missteps in this area can result in regulatory issues, employee dissatisfaction, and operational delays. Businesses may handle these developments with confidence if they use good payroll management. Instead of just updating data, this requires coordinated communication with HMRC, accurate FPS and P11D form filing, and clear internal processes for handling deductions, tax codes, and personnel records.
Your payroll management strategy will determine the success of a full-scale integration or partial scheme transfer. Mergers and acquisitions payroll companies face huge stakes. Payroll accuracy during major changes protects your company’s brand, assures compliance, and stabilizes employee relations.