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The pay run wizard takes you from a blank period to a locked, reported payroll in seven steps. Each step is reachable at any time from the horizontal step bar at the top of the screen. Use the Previous and Next buttons at the bottom to move between steps, or click a step directly to jump to it.
Before running your first pay run, make sure your organisation settings, at least one pay run schedule, and your people are all set up. See getting started if you haven’t done that yet.
Pay runs in progressPay runs in progress

The Pay runs area

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Starting a pay run

Go to Pay runs in the main navigation. The page shows pay runs in progress, grouped by pay frequency. Select Open next pay run (or Start new pay run if this is your first). A confirmation modal shows the suggested pay schedule, tax year, and period — and lets you override the payment date if needed. Confirm, and the wizard opens at step 1.
Flow Payroll suggests the next sequential period automatically. You must lock the current period before rolling into a new tax year.

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The seven wizard steps

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Step 1 — Payments

The payments step is a split-panel view: the employee list on the left, pay lines for the selected employee on the right.Reviewing what’s already thereEvery employee on the pay schedule appears with their calculated payslip. Statutory pay (SSP, SMP, SPP, and so on), recurring payments, and court-order deductions that were set up on the employee’s profile are already applied. Select an employee to inspect their individual lines.Adding a one-off payment or deductionSelect an employee, then choose Add payment or Add deduction. Pick the pay element, enter the amount and quantity, and save. The payslip recalculates immediately.Adjusting pension for this run onlyFor an enrolled employee, the small arrow next to Add deduction opens a menu with a Pension section: One-off additional voluntary contribution and Override pension this run. Both apply to this pay run only and leave the scheme settings alone. See pension contributions and refunds.Importing in bulk from CSVIf you have many lines to enter, click Import CSV in the pay run’s top bar to bring them in from a CSV or Excel file — hours exports, bonus lists, or a full payments file from another system. See importing payments from CSV below for the columns, the wide layout for one-row-per-employee files, and tagging imported lines.Alert filtersThe search bar and alert-code chips above the employee list let you filter to employees with specific issues — for example, employees flagged for a pension alert. Clicking through from the Alerts step (step 2) pre-filters the list automatically.
Statutory payments, pension contributions, and court-order deductions are calculated automatically. You do not need to enter them manually here. See statutory payments, auto-enrolment, and court orders for more detail.
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Step 2 — Alerts

The alerts step surfaces anything that needs your attention before you lock the period.Alerts fall into two categories:
  • Blocking alerts — must be resolved before you can lock. These include employees who need to be enrolled into a pension but haven’t been yet, and similar compliance issues.
  • Advisory alerts — informational flags that you can acknowledge and proceed past.
Pension alerts show workers who are eligible for auto-enrolment but whose enrolment is not yet complete. You can enrol workers individually or in batch from here. Clicking Go to payments on a pension alert pre-filters the payments step to that worker.Leaver on this pay run flags employees whose leaving date is being reported to HMRC on this submission, so you can check the dates before you finalise. If someone left before this pay period even started, the alert is raised as a warning instead — that means the leaving date missed its own pay run and is only reaching HMRC now. See leavers.Once all blocking alerts are resolved the step shows a green summary and you can move to locking.

Auto-enrolment

How Flow Payroll assesses and enrols workers each pay run.
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Step 3 — Lock pay run

Locking finalises the period. Before you lock, review the summary information on this step:
  • The lock status card tells you whether the pay run is already locked or still open.
  • If unlocked, a list of what locking will do is shown: employee data and calculations are finalised, payslips are generated and can no longer be modified, RTI submission becomes available, and reporting documents can be generated.
Select Lock pay run and confirm the prompt. Locking is irreversible — you cannot edit pay lines after this point.Once locked, the step shows a success state with the lock date and the user who locked it.
Locking cannot be undone. Verify your payments and resolve all blocking alerts before locking.
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Step 4 — Payslips

After locking, this step shows the full payslip list for the period.
  • Search by employee name, payroll ID, NI number, or payroll code.
  • Select individual payslips or use Select all to select every employee shown.
  • View opens the payslip in a preview modal — payslips are marked Final once the period is locked, or Preview if viewed before locking.
  • Download saves an individual payslip as a PDF.
  • Download selected bundles the selected payslips into a single zip file.
  • Email payslips sends a notification to selected employees with a link to their payslip.

Payslips

What payslips show, how to share them, and how employees access them.
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Step 5 — RTI submission

This step manages your Full Payment Submission (FPS) to HMRC.Before submittingThe validation card confirms the pay run is locked and completed. The pay run summary card shows the total employee count, how many processed successfully, and how many (if any) failed.Generating a previewSelect Preview FPS to generate the FPS XML without submitting it to HMRC. Once the preview is ready, you can:
  • View preview — inspect the XML in a viewer panel.
  • Export PDF — download a formatted PDF report of the FPS data.
  • Export CSV — download the FPS data as a spreadsheet.
  • Regenerate preview — rebuild the preview after any late changes.
SubmittingSelect Submit FPS to HMRC and confirm. The submission status updates automatically every few seconds while HMRC processes the file. Once accepted, the status changes to Sent and the submission ID and date are shown.Final submissionFor the last pay period of the tax year, the Final submission toggle is pre-enabled. You can also enable it manually and specify whether the scheme is ceasing. Only mark a submission as final on the last FPS of the tax year — incorrect use can cause HMRC processing issues.If submission failsThe status changes to Failed and any error codes from HMRC are listed. Correct the underlying issue, then resubmit. If HMRC returns a “final submission required” response, a form appears asking you to confirm the final submission details before resubmitting.
The FPS must reach HMRC on or before your pay day. Late submissions may attract a penalty.

HMRC & RTI

FPS, EPS, resubmissions, and HMRC notices.
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Step 6 — Reporting and documents

This step provides access to the reports and documents generated from the period’s payslip data. Download or view the reports you need for your finance team, pension provider, or audit records.
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Step 7 — Summary

The summary step shows the totals for the completed pay run:The detailed breakdown expands into gross pay, net pay, PAYE deductions, student loan, postgraduate loan, NI split by employee/employer/Class 1A, and pension contributions split by employee/employer.If a pay run checklist is enabled for your organisation, it appears here so you can mark off your end-of-period tasks before closing.

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Importing payments from CSV

Click Import CSV in the pay run’s top bar (available while the pay run is unlocked) to bulk-load payment lines from a CSV or Excel (.xlsx) file. The importer runs on Flow Payroll’s shared import wizard — map your columns once, click Save Mapping, and every future import from the same file structure is recognised automatically. See importing data from CSV for the wizard itself; this section covers what’s specific to payments.
Import Payments from CSV modal open on a pay run

Importing payments into an open pay run

Deductions import through the same flow — a line whose pay element is a deduction element is applied as a deduction on the payslip.

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Mandatory columns

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Optional columns

Template (identical to the wizard’s Download template):
Download payroll_lines_import_template.csv

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Wide layout — one row per employee

Many payroll exports put each employee on a single row with one column per pay element — Overtime Hours, Bonus, Mileage — rather than one row per line. Flip on Wide layout (many line items per row) at the top of the mapping step to import these files directly.
Wide layout mapping with the pay element columns panel

Wide layout — each pay element gets its own column mapping

In wide layout, a Pay element columns panel replaces the per-line amount fields. Click Add column for each pay element in your file, then pick its Units column and/or Amount column (each with an optional default), plus an optional description. Every row then fans out into one payment line per pay element that has a value. Skip line items where units are 0 or blank is on by default, so an employee with no overtime this period simply gets no overtime line — you can import the full sheet without creating empty lines.

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Tag mappings

To tag every imported line — by site, project, cost centre, or any other dimension — expand Tag mappings at the bottom of the mapping step and click Add tag. Pick a tag group and name (you can create new ones on the spot), then either map a CSV column to supply the value per row or set a fixed value for all rows.
Tag mappings section of the payments import

Tag mappings attach tags to every imported line

Tag mappings, wide-layout settings, defaults, and column matches are all part of the saved mapping, so a saved payments mapping restores the whole setup in one click.

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Pay run statuses

The FPS status is shown as a separate badge alongside the pay run status: FPS not sent, FPS sending, FPS sent, or FPS failed.

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How statutory pay, pensions, and court orders fold in

You do not need to calculate or enter these manually:
  • Statutory payments (SSP, SMP, SPP, and so on) — set up on the employee’s profile and applied automatically each period they are applicable.
  • Pension contributions — assessed and calculated automatically each period based on the worker’s enrolment status and the contribution rates on your pension configuration.
  • Court orders — deducted automatically according to the order type, rate, and protected earnings threshold configured on the employee.
All three appear as line items in the payments step so you can verify them. The alerts step surfaces any pension compliance issues that need resolution before locking. Pension shows as one line per contribution, labelled Pension, Additional voluntary contribution, One-off additional voluntary contribution or Pension refund, with a note saying how each was worked out. See pension contributions and refunds.

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Where to go next

Payslips

Preview, download, and send payslips to your employees.

HMRC & RTI

Submit your FPS, file your EPS, and handle resubmissions.

Statutory payments

SSP, SMP, SPP, and other statutory pay types.

Auto-enrolment

Pension assessment, enrolment, and contributions.