Run payroll and file RTI to HMRC
Process the next pay run, send the Full Payment Submission to HMRC under Real-Time Information, and produce payslips and pension contributions from the YionStack payroll module.
In this guide
Payroll- Steps
- 6
- Prereqs
- 4
- Pitfalls
- 4 common ones
- Related
- 3 guides
Walkthrough only — no setup wizard. The flow is exactly what you do inside YionStack today.
Before you start
- Employees onboarded with valid NI number, tax code and starter declaration.
- A PAYE scheme (Office Number / PAYE Reference / Accounts Office Reference) set in Settings → Payroll.
- HMRC online services credentials (Gateway User ID + password) entered in Settings → Integrations → HMRC for RTI submission.
- Pension scheme (Smart, People’s Pension or NEST) configured if any employee is auto-enrolled.
Steps
- 1
Open the payroll workspace
Go to Payroll → Runs. The page shows the next scheduled run with its pay date, frequency, employees included and projected total cost (gross pay + employer NIC + employer pension).
- 2
Open the new run
Open the upcoming run. YionStack loads each employee’s recurring pay elements (salary, hourly rate, allowances) and applies year-to-date tax codes, NI categories and student loan deductions from HMRC notices on file.
- 3
Add variable elements
Add overtime, bonuses, commission, statutory pay (SMP, SSP, SPP), expense reimbursements, or salary sacrifice changes for this period. The payslip preview recalculates as you edit.
- 4
Review payslips
Review each payslip for the period. Net pay, tax, NI, pension and any deductions are shown line by line. Flag anything unexpected; YionAI compares against the previous three runs and highlights variances larger than 15%.
- 5
File the FPS to HMRC
Approve the run. YionStack submits the Full Payment Submission (FPS) to HMRC over the GovTalk RTI channel before payday (so the submission is on time). HMRC responds with a submission reference that attaches to the run.
- 6
Send payslips and pay employees
Once HMRC has accepted the FPS, the payslips email to employees through the YionStack mail service. The bulk-payment file (Bacs or Faster Payments via Modulr) generates for upload to your bank; the employer pension contribution lodges with the pension provider.
Common pitfalls
Filing late
HMRC charges late-filing penalties for an FPS sent after the pay date. YionStack flags any run that has not been filed 24 hours before the pay date; approve before the deadline to stay penalty-free.
Leaver dates
A leaver needs their leaving date set before the final run; otherwise their P45 cannot be issued and the next FPS will still include them. YionStack prompts for the date when you mark an employee as leaving.
New starter without P45
For a starter without a P45, set the starter declaration (A, B or C) before the first run. Without it, the FPS will be rejected as malformed and the run will not file.
Pension contribution mismatch
If the pension provider rejects the contribution upload (mismatched NI number or scheme reference), the FPS is still accepted by HMRC, but the contribution lodges as failed. Fix on the pension provider side and retry from the run record.
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