Registered as an employer: what happens before your first payroll?

Registered for PAYE? You are not payroll-ready yet

Submitting an employer registration starts the PAYE setup process. It does not, by itself, make the employer ready to run and report its first payroll.

Before the first payroll is fully operational, the employer must be able to:

1. identify the correct legal employer and preserve the registration evidence;
2. recognise the references and activation information HMRC sends;
3. configure maintained payroll software with the correct employer details;
4. collect and validate the employee’s starter and pay information;
5. calculate, review and approve payroll for the real contractual payday;
6. pay the employee and produce a payslip; and
7. send the required Full Payment Submission (FPS) to HMRC.

These are connected steps, but they are not the same event. In particular, paying an employee and successfully reporting that payment to HMRC are separate actions.

GOV.UK explains how to register as an employer. This guide explains how to manage the waiting period, understand what arrives and reach the first payday safely.

Identify what HMRC has sent you

Employer PAYE correspondence contains several items with different purposes. Do not treat them as interchangeable.

The examples below are fictitious format examples only. They are not live employer credentials and must never be entered into payroll software or used in a submission.

Item	What it looks like	What it is for	Who normally receives it	Where it is entered or retained	When it is first needed	If it is missing
Employer PAYE reference	Fictitious example: 123/AB456	Identifies the PAYE scheme in RTI reporting and HMRC correspondence. The first three digits are the HMRC office number; the part after the slash is the employer reference.	The employer, or the accountant or tax adviser if they registered on the employer’s behalf	Enter the two parts in the corresponding employer fields in payroll software; retain the HMRC letter securely	Before an FPS or EPS can be completed and sent for the scheme	Check who submitted the registration and where correspondence was directed; use HMRC’s current response-time route rather than guessing a reference
Accounts Office reference	Fictitious example: 123PA00012345	Identifies the employer account in RTI information and is used to allocate PAYE payments to the correct HMRC account	The employer, accountant or tax adviser receiving the registration correspondence	Enter it in the employer or HMRC payment settings in payroll software and retain it with the scheme record	It appears in RTI employer information and is needed when arranging and identifying payments to HMRC	Check the registration letter and PAYE Online account when accessible; do not substitute the employer PAYE reference
PAYE Online activation code	A postal activation code; do not copy or photograph it into an open payroll procedure	Activates PAYE Online so the employer can view liabilities, payments, notices and alerts	The address associated with the online enrolment	Use it in the HMRC online activation process; store only the access and recovery ownership record afterwards	HMRC says the code should arrive within 10 days after online registration and must be used within 28 days of the date on the letter	Enrol for PAYE Online again if the code expires; confirm the registered address and access owner if it does not arrive
Application or registration confirmation	Submission receipt, confirmation page or saved application evidence	Proves what was submitted, by whom and when	The person who completed the application	Retain with the submitted legal-entity details and expected first payday	Immediately after applying and throughout the waiting period	Ask the submitter for the evidence; confirmation is useful but is not a substitute for the PAYE or Accounts Office references

HMRC’s payroll information guidance explains the employer fields reported through RTI. Its PAYE Online guidance explains enrolment, activation and what the online service can be used for.

Where are you now?

Answer these questions in order. Stop at the first “no” that prevents the next action, then follow the matching route below.

1. Has the employer registration been submitted?
2. Has the first payday happened?
3. Has the employer PAYE reference arrived?
4. Has the Accounts Office reference arrived?
5. Is PAYE Online activated?
6. Has payroll software been configured and tested?

Preparing to register

Next action: confirm whether registration is required, identify the legal employer, choose the real expected first payday and submit within HMRC’s permitted window.

Preserve: the status and registration decision, legal-entity information, expected first payday, application answers and submission confirmation.

Still possible: choose the payroll operating model, collect starter information and prepare a controlled payroll calendar.

Blocked: a live FPS cannot be sent for a scheme that has not been registered and issued the required employer identifiers.

Use Check who belongs on payroll and register for PAYE for the registration decision itself.

Application submitted and references are still outstanding

Next action: record who receives HMRC post, monitor the expected response using HMRC’s maintained service and continue preparing the first payroll.

Preserve: submission evidence, submitted employer details, real first payday, correspondence address and the named person responsible for checking arrivals.

Still possible: configure non-reference employer settings, validate employee information, build approved pay inputs, test calculations without submitting live data, and plan the payment and review controls.

Blocked: do not complete a live RTI submission using a guessed, fictitious or borrowed identifier.

HMRC directs employers to its weekly updated response-time checker. Because that estimate can change, this guide does not promise that employer registration will be processed in a fixed number of days.

Both employer references have arrived before payday

Next action: independently verify the legal entity and both references, enter them in payroll software, activate PAYE Online and complete the controlled first-payroll setup.

Preserve: the original HMRC correspondence, a verified configuration record, payroll test evidence and the named approver.

Still possible: complete the normal first-payroll route and send the FPS on or before payday.

Blocked: live processing remains blocked if the software configuration, employee record, calculation or approval is incomplete.

Payday is approaching but the employer PAYE reference has not arrived

Next action: protect the real payday. When registration was submitted before payday and the reference is still outstanding, HMRC says to run payroll, store the FPS and send it late after the reference arrives.

Preserve: registration evidence, real payday, approved employee inputs, payroll calculation, payslip, employee-payment evidence, stored FPS, reference-arrival date, eventual submission receipt and any HMRC response.

Still possible: calculate and review payroll, pay the employee on the contractual date, issue the payslip and store the full submission in maintained payroll software.

Blocked: the FPS cannot be successfully completed and sent for the new scheme until the required employer PAYE reference has arrived.

Follow Late PAYE registration: can you run payroll before your PAYE reference arrives? for the precise stored-FPS route and its boundaries.

Payday has already happened

Next action: first establish whether registration had been submitted and whether an FPS was stored or attempted. Reconcile the actual payment, payroll output, registration evidence and every submission response before doing anything again.

Preserve: the factual payment date and value, employee record, payslip, calculation, registration status, stored or attempted reports and HMRC responses.

Still possible: preserve the history, obtain the references and use maintained HMRC, payroll-software or professional guidance to determine the correct reporting action.

Blocked: do not guess another FPS, duplicate a report, move the payment into a later payroll or rewrite the actual payday. If registration had not been submitted before payday, this is a catch-up question rather than the supported waiting-for-reference route.

The activation code is missing or expired

Next action: confirm whether registration was completed online, check the correspondence address and access owner, then repeat PAYE Online enrolment if the 28-day activation window has expired.

Preserve: enrolment dates, delivery address checks, access ownership and the successful activation record.

Still possible: retain and configure verified employer references and continue preparing payroll. PAYE Online activation and payroll-software RTI credentials are related controls, but they should not be assumed to be the same login or setup step.

Blocked: PAYE Online functions such as viewing liabilities, payment history, employee notices and service alerts remain unavailable until access is activated.

An accountant registered the employer

Next action: obtain a written handoff showing which correspondence has arrived, which references were verified, who controls PAYE Online and who will perform each first-payroll action.

Preserve: the registration confirmation, both employer references, access and recovery ownership, software configuration evidence, submission receipts and payroll reports.

Still possible: delegate preparation or reporting under an agreed responsibility map.

Blocked: payroll approval should not rely on an assumption that “the accountant has everything.” The employer must know who holds each dependency and how evidence will be returned.

Protect the first payday while you wait

The highest-risk mistake is treating a delayed HMRC letter as a reason to make the first payment informal. The employment payment still needs an approved payroll calculation, a real payment date, a payslip and a complete evidence trail.

When employer registration was submitted before the first payday but the employer PAYE reference has not arrived, HMRC’s stated route is:

1. run payroll for the actual payday;
2. store the full payment submission; and
3. send the late FPS when the employer PAYE reference arrives.

This is a narrow first-registration route. It does not remove the normal requirement to send an FPS on or before payday in routine payroll.

Keep one first-payday evidence pack containing:

• the employer-registration submission and expected payday;
• the contractual and actual payment date;
• verified employee and starter information;
• approved gross-pay inputs and payroll calculation;
• payslip and employee-payment evidence;
• the stored FPS and its software status;
• the date each HMRC reference arrived;
• the later FPS submission receipt and response; and
• notes of any HMRC or professional guidance relied upon.

Turn the references into a working payroll

Receiving the letters removes important blockers, but the references still need to be verified and used correctly.

Configure the employer record

Enter the employer PAYE reference using the payroll software’s HMRC office-number and employer-reference fields. Enter the 13-character Accounts Office reference in the employer or HMRC payment field specified by the maintained software. HMRC lists both as employer information reported in every FPS and EPS.

Have a second authorised person compare the saved settings with the original HMRC correspondence. Do not verify a value by comparing it with another transcription of the same value.

Activate and control PAYE Online

An employer that registers online is automatically enrolled for PAYE Online. HMRC says it sends the activation code by post within 10 days. The account must be activated within 28 days of the date on the letter; after that, the employer must enrol again.

Record who controls the account, who can recover access and who reviews liabilities, payments, tax-code notices and late-reporting alerts. Do not place passwords or activation codes in an open payroll procedure.

Complete the first-payroll handoff

Before approving the first payday:

1. verify the employer record and both references;
2. complete the employee record using a P45 or starter checklist as appropriate;
3. configure the pay frequency and actual payment date;
4. test the software without sending invented or dummy employee data to HMRC;
5. calculate and review the complete payroll population;
6. approve the employee payment and payslip;
7. send the FPS on or before payday, or document the supported stored-FPS route;
8. retain the submission response; and
9. prepare to reconcile and pay the resulting HMRC liability using the correct Accounts Office reference.

Continue with Choose a payroll method and complete setup, Add a new starter correctly and Produce payslips, pay employees and send FPS.

Confirm ownership when an accountant is involved

Using an accountant, payroll bureau or other agent can change who performs the work. It does not transfer the employer’s legal responsibility for PAYE.

Agree and record an owner for each control:

Control	Ownership question
HMRC correspondence	Which address receives it, and who checks it?
Employer references	Who records, verifies and returns both references to the employer?
PAYE Online	Who holds access, recovery details and responsibility for reviewing notices?
Payroll software	Who configures the employer and employee records?
Calculation and review	Who prepares payroll, and who independently approves it?
Employee payment	Who authorises and releases the actual payment?
FPS	Who sends it, checks the response and resolves a rejection?
HMRC payment	Who reconciles the liability, authorises payment and confirms allocation?
Evidence	Where are reports, payslips, submissions, responses and correspondence retained?

The employer should retain controlled access to its references, payroll reports, HMRC responses and continuity arrangements. A service agreement that says “we run payroll” is not specific enough to answer who approves pay, sends FPS or pays HMRC.

First-payday readiness checklist

Interactive checklist

First-payday readiness after PAYE registration

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• Employer-registration evidence retained
• Real contractual first payday recorded
• Employer PAYE reference verified or waiting status documented
• Accounts Office reference verified or waiting status documented
• PAYE Online activated or access action assigned
• Payroll software configured and independently checked
• Employee starter record complete
• Payroll calculation reviewed and approved
• Payslip and employee-payment plan confirmed
• FPS submission or supported storage route documented
• Submission and response evidence owner assigned
• HMRC liability and payment process assigned
• Accountant or bureau responsibilities confirmed in writing

Once the employer references, employee data, approved pay and reporting responsibilities are controlled, Workmax can help connect them into a repeatable payroll workflow. Software supports the calculation, approval, reporting and payment evidence; the employer remains responsible for the decisions and deadlines.

Sources and review

Reviewed July 2026 by the Workmax payroll team. This is general UK payroll information, not tax, legal or accountancy advice. Historic payments, missed registration, disputed employment status or uncertain submissions can require HMRC or qualified professional support.

• GOV.UK: Register as an employer
• GOV.UK: PAYE Online for employers
• GOV.UK: Check when to expect a reply from HMRC
• GOV.UK: Payroll information to report to HMRC
• GOV.UK: Setting up payroll
• GOV.UK: Reporting payroll to HMRC