## Zoho Payroll Documentation Index

Access the complete documentation index at:
https://www.zoho.com/uk/payroll/llms.txt

Use this file to discover all available documentation pages before proceeding.

# Regular Pay Runs

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A regular pay run follows your [pay schedule](/uk/payroll/help/employer/settings/pay-schedule.html). Zoho Payroll creates each pay period for you. You review the figures, approve the pay run, tell HMRC what you paid, then pay your employees.

For UK payroll, that usually means:

1.  Checking earnings, tax, National Insurance, pensions, and other deductions.
2.  Approving the pay run (or submitting it for someone else to approve).
3.  Submitting the **Full Payment Submission (FPS)** to HMRC. Zoho Payroll prepares this RTI report automatically from the approved pay run; you confirm the send to HMRC.
4.  Paying employees, for example by bank transfer using a Bacs file, or by recording a payment you’ve already made.

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## Process a Pay Run

1.  Go to **Pay Runs**.
2.  Under **Current Pay Runs**, open the pay run that is ready to process.
3.  Click **Process Pay Run** for the period shown.

![Process a ready pay run from Current Pay Runs](/payroll/help/uk/pay-runs/pay-runs-current-ready.png)

The pay run opens in **Draft** so you can review it. Complete approval before the **pay date**, which is the day employees should receive their pay. You can edit the pay date from the summary if needed.

![Regular payroll draft with employee summary](/payroll/help/uk/pay-runs/regular-payroll-draft-employee-summary.png)

If the pay date has passed, Zoho Payroll shows that the payment is overdue. A late FPS may incur an HMRC penalty, so approve and submit as soon as you can.

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## Review a Pay Run

Check the summary at the top of the pay run:

**Item**

**What it shows**

**Payroll Cost**

The overall cost of the pay run before you focus on take-home pay.

**Total Net Pay**

The total take-home pay for all employees in this period, after tax, National Insurance, pensions, and other deductions.

**Pay Date**

The date employees are paid.

**Pay Run Summary**

A breakdown including **Tax & National Insurance**, **Pension Contributions**, and **Deductions**.

Use the tabs under the summary to move between **Employee Summary**, **Tax Summary**, **Pensions & Deductions Summary**, and **Benefits in Kind Summary**.

**Tax & National Insurance** covers Income Tax under Pay As You Earn (PAYE) and National Insurance contributions. PAYE is how you deduct Income Tax from employees’ pay and pay it to HMRC. National Insurance funds state benefits such as the State Pension.

**Pension Contributions** are the workplace pension amounts calculated for this pay run for employees and, where applicable, your organisation.

In the **Employee Summary** list you can:

*   Review each employee’s hours, gross pay, deductions, pensions, **Tax & NI**, and net pay.
*   Open an employee to see taxable pay, Income Tax (PAYE), National Insurance, pensions, student loans, and other deductions.
*   Add earnings or deductions for that employee in this pay run, then save to update net pay.

![Employee pay details in a regular pay run](/payroll/help/uk/pay-runs/regular-payroll-employee-pay-drawer.png) ![Add an earning for an employee in a pay run](/payroll/help/uk/pay-runs/employee-pay-add-earning.png) ![Add a deduction for an employee in a pay run](/payroll/help/uk/pay-runs/employee-pay-add-deduction.png)

**Pro Tip:** After you add an earning or deduction in the employee pay drawer, click **Save** so Zoho Payroll recalculates net pay for that employee before you approve the pay run.

![Deduction added in employee pay details pending save](/payroll/help/uk/pay-runs/employee-pay-fines-added.png)

**Pro Tip:** Use **Search Employees** above the employee list to jump straight to someone when the pay run is large.

![Search employees in a regular pay run](/payroll/help/uk/pay-runs/regular-payroll-search-employees.png)

**Pro Tip:** Open the **Active Employees** dropdown to switch between views such as all employees, skipped employees, yet to pay, or paid. Use the filter to narrow by employee type, or open **\+ More Filter** for work location, department, or job title.

![Active Employees dropdown on a regular pay run](/payroll/help/uk/pay-runs/regular-payroll-active-employees-dropdown.png) ![Filter employees by employee type in a pay run](/payroll/help/uk/pay-runs/regular-payroll-filter-employee-type.png) ![More filters for work location, department, and job title](/payroll/help/uk/pay-runs/regular-payroll-filter-more-work-location.png)

**Pro Tip:** Open **Comments** from the pay run toolbar when you need to leave a note for another approver or keep a record of why you changed someone’s pay.

![Comments sidebar on a draft regular pay run](/payroll/help/uk/pay-runs/regular-payroll-draft-comments-sidebar.png)

### Tax Summary

The **Tax Summary** shows **Income Tax (PAYE)**, National Insurance, and related figures such as Class 1A NIC for the pay run. Use it to check totals before you approve.

![Tax summary for a regular pay run](/payroll/help/uk/pay-runs/regular-payroll-draft-tax-summary.png)

### Pensions & Deductions Summary

This summary lists pension schemes and other amounts taken from pay, such as:

*   **Pension schemes:** Workplace pension contributions for each scheme (for example Relief at Source or Salary Sacrifice groups).
*   **Student Loan (Plan 1)** or **Student Loan (Plan 2):** Repayments through payroll when the employee’s pay is above the repayment threshold for their plan.
*   **Postgraduate Loan:** Repayments of a postgraduate loan through payroll, where applicable.
*   **Attachment of Earnings** or similar deductions: Court or agency orders that require you to deduct money from an employee’s pay.

![Pensions and deductions summary for a regular pay run](/payroll/help/uk/pay-runs/regular-payroll-draft-pensions-deductions.png)

### Benefits in Kind Summary

If your organisation reports benefits in kind through payroll, review the **Benefits in Kind Summary**. This can include items such as car and fuel benefit or mileage allowance, and related Class 1A NIC.

![Benefits in kind summary for a regular pay run](/payroll/help/uk/pay-runs/regular-payroll-draft-benefits-in-kind.png)

### Apply Changes to Employee Pay

If you’ve changed an employee’s pay after this pay run was created, Zoho Payroll will not use those new figures until you apply them.

1.  Review the message that you’ve changed employee pay since this pay run was created.
2.  Click **Apply Changes** to recalculate and update this pay run.

### Skip an Employee from This Pay Run

If someone should not be paid in this period:

1.  Click the action icon next to the employee.
2.  Select **Skip from this payroll**.
3.  Enter a reason, then confirm.

![Skip an employee from this payroll](/payroll/help/uk/pay-runs/regular-payroll-skip-from-payroll-menu.png) ![Enter a reason when skipping an employee from payroll](/payroll/help/uk/pay-runs/skip-employee-reason-dialog.png)

**Pro Tip:** To skip or add several people at once, select the employees in the list, then use **Skip from this payroll** or **Add to payroll** above the table.

![Bulk skip or add employees in a pay run](/payroll/help/uk/pay-runs/regular-payroll-bulk-skip-add.png)

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## Import and Export Pay Run Data

Use **Import / Export** above the employee list when you need to update hours and earnings in bulk, or download payroll data from the pay run.

**Pro Tip:** Choose **Import > Employee Hours & Earnings** when many employees have variable hours or earnings for the period. Export first if you want a template-style file to fill in.

![Import employee hours and earnings for a pay run](/payroll/help/uk/pay-runs/regular-payroll-import-employee-hours.png)

**Pro Tip:** Choose **Export > Payroll Data** when you need a file of this pay run for checks outside Zoho Payroll, or before you make bulk edits.

![Export payroll data from a pay run](/payroll/help/uk/pay-runs/regular-payroll-export-payroll-data.png)

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## Workplace Pension Tasks in a Pay Run

During a pay run, Zoho Payroll may show a task when employees are eligible for workplace pension auto-enrolment. Click **View Employees**, then:

*   **Enrol** the employee into a contribution group with your [pension provider](/uk/payroll/help/employer/pensions/).
*   **Postpone** enrolment for up to three months.
*   **Mark as Exempt** when the employee qualifies for an exception.

![Employees eligible for a workplace pension plan](/payroll/help/uk/pay-runs/employees-eligible-workplace-pension.png) ![Enrol an employee into Nest from a pay run](/payroll/help/uk/pay-runs/enroll-employee-nest-pension.png) ![Postpone workplace pension enrolment](/payroll/help/uk/pay-runs/postpone-workplace-pension-enrollment.png) ![Mark an employee as exempt from auto-enrolment](/payroll/help/uk/pay-runs/mark-employee-exempt-auto-enrolment.png)

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## Approve a Pay Run

Approval locks in the pay run so you can move on to reporting and payment.

Depending on your role:

*   If you can approve pay runs, click **Approve** or **Submit and Approve**.
*   If you cannot approve pay runs, click **Submit for Approval**. An authorised user then reviews and approves it.

![Submit a pay run for approval](/payroll/help/uk/pay-runs/regular-payroll-submit-for-approval.png) ![Approve a pay run when you have approval permission](/payroll/help/uk/pay-runs/regular-payroll-draft-approve.png)

Before you confirm, Zoho Payroll asks you to make sure the pay details are correct. Once approved, you can pay your employees or record a payment.

![Confirm approving a pay run](/payroll/help/uk/pay-runs/approve-pay-run-confirmation.png)

**Warning:** Once a pay run is approved, you cannot edit it in the usual way. Check the figures carefully before you approve.

### Reject a Pay Run

If a pay run was submitted for approval and should not go ahead, an authorised user can reject it. Open the **More** menu on the pay run, select **Reject**, enter a reason, and confirm.

![Reject a payroll with a reason](/payroll/help/uk/pay-runs/reject-payroll-reason-dialog.png)

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## Submit the FPS to HMRC

After approval, the pay run moves to **Payment Due**. Zoho Payroll has already prepared a **Full Payment Submission (FPS)** from that pay run. An FPS is part of Real Time Information (RTI). It tells HMRC, for each employee, what you paid and what you deducted on or before the pay date.

Next, submit that FPS to HMRC (or mark it as submitted if you sent it another way). You do not need to create the FPS file separately.

For what an FPS includes and when it is due, refer to the [GOV.UK guidance on payroll information to report to HMRC](https://www.gov.uk/guidance/what-payroll-information-to-report-to-hmrc). Employer-level claims and nil periods use an [Employer Payment Summary (EPS)](/uk/payroll/help/employer/forms/employer-payment-summary.html) in [Forms & Filing](/uk/payroll/help/employer/forms/).

![Payment due pay run with FPS ready to submit to HMRC](/payroll/help/uk/pay-runs/regular-payroll-payment-due-fps-ready.png)

1.  Open the approved pay run. Zoho Payroll shows that the FPS is ready to submit.
2.  Click **Submit to HMRC**.
3.  Enter your **Government Gateway** user ID. This is the login HMRC gives your organisation for online tax services.
4.  Complete the submission.

### Late FPS

HMRC expects the FPS on or before the pay date. If that date has passed, Zoho Payroll asks you to select a reason for the late submission before you continue.

![Submit FPS to HMRC with late submission reason](/payroll/help/uk/pay-runs/fps-submit-to-hmrc-late-reason.png)

If a pay run is overdue, you may also see a warning that a late FPS may incur an HMRC penalty. Submit as soon as you can and keep the reason accurate. For official FPS timing, refer to the [GOV.UK guidance on reporting to HMRC (FPS)](https://www.gov.uk/running-payroll/reporting-to-hmrc).

### Mark FPS as Submitted

If you’ve already sent the FPS to HMRC outside Zoho Payroll (for example from another system):

1.  Click **Mark as Submitted**.
2.  Confirm in the dialog.

![Mark FPS as submitted outside Zoho Payroll](/payroll/help/uk/pay-runs/fps-mark-as-submitted-dialog.png)

When HMRC has accepted the FPS, Zoho Payroll shows that the FPS for this pay run has been submitted to and accepted by HMRC.

![FPS submitted to and accepted by HMRC](/payroll/help/uk/pay-runs/regular-payroll-payment-due-fps-accepted.png)

### Download or Undo the FPS

From the **More** menu on a payment-due or paid pay run, you can:

*   **Download FPS file** for your records.
*   **Undo FPS Submission** if you need to reverse a submission recorded in Zoho Payroll (confirm when prompted).

![More menu with Download FPS file on a payment due pay run](/payroll/help/uk/pay-runs/regular-payroll-payment-due-more-menu.png) ![Confirm undoing an FPS submission](/payroll/help/uk/pay-runs/undo-fps-submission-confirmation.png)

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## Record Payment

After the pay run is approved, you pay employees or record that you’ve already paid them. On a **Payment Due** pay run, use **Mark as Paid**. Employee rows can also show **Yet To Pay** with a line-level mark-as-paid action.

**Note:** If you haven’t submitted the FPS for this pay run yet, Zoho Payroll asks you to submit it to HMRC before you record payment. That keeps payment records aligned with what you’ve reported to HMRC.

![Submit FPS before recording payment](/payroll/help/uk/pay-runs/fps-required-before-payment-warning.png)

### Download a Bacs File

**Bacs** (Bankers’ Automated Clearing Services) is the UK system many employers use to pay salaries straight into employees’ bank accounts. Instead of paying each person manually, you upload a payment file to your bank.

If you pay by Bacs, click **Download Bacs File** from the pay run summary, then upload it through your bank or banking software so the net pay can be sent to each employee.

### Mark as Paid / Record Payment

1.  Click **Mark as Paid**.
2.  Enter the payment date and payment mode.
3.  Choose whether to notify employees about their payslips, then confirm.

![Record payment for a pay run](/payroll/help/uk/pay-runs/record-payment-dialog.png)

When payment is recorded, the pay run shows as **Paid**.

![Regular payroll marked as paid](/payroll/help/uk/pay-runs/regular-payroll-paid-summary.png)

### Delete a Recorded Payment

If you recorded a payment by mistake, open the **More** menu on the paid pay run, select **Delete Recorded Payment**, and confirm. Zoho Payroll warns that this can affect tax liabilities for the period.

![Download FPS file or delete recorded payment on a paid pay run](/payroll/help/uk/pay-runs/regular-payroll-paid-download-fps-menu.png) ![Confirm deleting a recorded payment](/payroll/help/uk/pay-runs/delete-recorded-payment-confirmation.png)

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## Pay Run History

Processed pay runs appear under **Pay Run History**. Learn more in [Pay run history](/uk/payroll/help/employer/pay-runs/pay-run-history.html).