## Documentation Index

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

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

# Pay Runs

* * *

Pay run refers to the act of compensating your employees for the days they’ve worked in a month. Using Zoho Payroll, you can process pay runs for your employees effectively.

Before you run payroll, make sure that you have set up the app and [added all your employees](/en-om/payroll/help/employer/employees/overview.html#add-employees).

## How to process a pay run?

Based on your pay schedule, you will receive a reminder for the pending pay runs. You can create a pay run from **Home** or **Pay Runs** module by clicking the **Create Pay Run** button.

![Create Pay Run](/payroll/help/en-om/payruns/create-pay-run.png) ![Create Pay Run](/payroll/help/en-om/payruns/payrun-details.png)

*   Click each employee name to add **Loss of Pay (LOP) days, LOP Reversal one-time earnings** and **one-time deductions**.
    
*   You can also import the LOP details for all employees in a CSV file instead of entering them one at a time. Click **Import/Export > LOP Details** or **Import/Export > One-time Earnings and Deductions**. You can also import and export the payroll details from here.
    

![Create Pay Run](/payroll/help/en-om/payruns/payrun-import.png)

*   You can also enter the overtime hours for the employee, if you’ve configured the Overtime Allowance component which has custom formula as the calculation type. However, if you have integrated with Zoho People, the overtime hours will be synced automatically if overtime hours sync is enabled.
    
*   If an employee doesn’t belong to the pay run, you can remove them by clicking the **…** icon next to the employee and selecting **Skip from Payroll**.
    

![Create Pay Run](/payroll/help/en-om/payruns/skip-payrun.png)

*   Add notes by clicking the **Comments** button in the top-right corner of the Pay Runs page.
*   Click the **Deductions** tab to view a summary of contributions made.

![Create Pay Run](/payroll/help/en-om/payruns/payrun-deduction.png)

### Withhold, Revert and Release Salary

There may be instances where you need to withhold your employee’s salary and disburse it in the following month or later. Our app supports withholding of employees’ pay for a certain period using the Salary Withhold option in the **Pay Runs** module. 

_When can your employee’s salary be withheld?_

Salary withhold can be applied when you have:

*   New employees who’ve joined at the end of a month.
*   Employees who are serving the notice period.

**Withhold Salary**

Here’s how you can withhold and release an employee’s salary in our app:

*   Go to the **Pay Runs** module.
*   Click **Create Pay Run**.
*   In the pay run draft, click the **More** icon (…) next to the employee’s name and click **Withhold Salary**.
*   Enter the reason for withholding the salary and click **Proceed**.

![Create Pay Run](/payroll/help/en-om/payruns/withhold-salary.png)

*   If you have enabled Zoho Books integration, you can choose to post the journal entry for the payroll transaction in Zoho Books. The transaction will be recorded under the account you had configured while setting up the integration.
*   After the pay run is approved, you can record payment on or after the payday.

**Note:** The social security benefits applicable to employee will be calculated and deducted from the employee’s salary when the salary is withheld. Only the Net Pay will be withheld when you apply salary withhold.

The withheld salary (only the net pay) can be released in the subsequent pay runs.

**Releasing Withheld Salary**

Let’s say you want to release the withheld salary along with the following month’s salary. Here’s how you can do it:

*   Go to the **Pay Runs** module.
*   Click **Create Pay Run**.
*   In the pay run draft, click the **More** icon (…) next to the employee’s name and click **Release** **Withheld** **Salary**.
*   You will be prompted to select the months for which the salary needs to be released. Once you’ve selected the months, the total payable amount will be displayed.
*   Click **Proceed**.

The withheld net pay will be released and added to the current month’s net pay.

**Note:** You cannot release a previously withheld salary if the current month’s salary is put on hold.

**Reverting Salary Withhold**

If you want to process a withheld salary in the same pay run, you will have to revert the salary withheld. Here’s how:

*   Go to the **Pay Runs** module.
*   Click **View Details** to view the pay run draft.
*   Click the **More** icon (…) next to the employee’s name and click **Revert Salary Withhold**.

![Create Pay Run](/payroll/help/en-om/payruns/revert-withheld-salary.png)

*   You will be prompted to confirm your actions. Click **Yes** to confirm.

The employee’s salary will be processed in the current month’s pay run.

*   Once you’ve added all the inputs, click the **Submit and Approve** button in the top-right corner of the page. If the user doesn’t have approval permission, they can simply submit the pay run. It will be approved or rejected post review by a user with approval access.

![Create Pay Run](/payroll/help/en-om/payruns/submit-and-approve.png)

*   If you have enabled Zoho Books integration, you can choose to post the journal entry for the payroll transaction in Books. The transaction will be recorded under the account you had configured while setting up the integration.
*   After the pay run is approved, you can record payment on or after the payday.
*   Click **Download Bank Advice** to download the bank advice, which helps you manually transfer the salaries to your employees’ bank accounts.
*   Click **Download Wage file** to download the wage file and submit it to the Wages Protection System (WPS) manually.

![Create Pay Run](/payroll/help/en-om/payruns/payrun-sif.png)

*   If you’ve made mistakes in an approved pay run, you can reject the approval and recall the pay run, provided you haven’t recorded payment for it.

**Note:** If you haven’t recorded payment for the pay run of a particular month, you can still create and process the pay run for the next month. However, you can only record payments for a payroll when all payments have been recorded for all past pay runs.

![Create Pay Run](/payroll/help/en-om/payruns/reject-payrun.png)

The journal entry posted in Zoho Books will be reversed and the transactions will be removed from the respective accounts.

* * *

## How to make selective payments?

Pay Runs module supports making payments for selective employees. You can make payments for a few of your employees on a certain date and pay the rest of your employees later.

To pay a few selected employees:

*   Go to the **Pay Runs** module.
*   Click **Create Pay Run**. 
*   Once you’ve added deductions, LOP details, etc., click **Submit and Approve**.
*   In the approved pay run, select the boxes next to the name of the employees’ for whom you want to make the payment. Make sure that these employees have the same payment mode.

![Create Pay Run](/payroll/help/en-om/payruns/selective-payments.png)

*   Choose **Record Payment** for selected employees .

![Create Pay Run](/payroll/help/en-om/payruns/record-selection.png)

*   You can select the payment date and click **Confirm**.

The selected employees will be marked as paid. You can make payments to the other employees on a different date and record the payment.  Journal entries corresponding to each payment will be posted automatically in Zoho Books along with the payment date.

* * *

### Download payslips?

Once you’ve processed the payroll, you can download all the related payslips.

*   To download the payroll documents, click **More** > **Download all Payslips**.

![Create Pay Run](/payroll/help/en-om/payruns/download-payslips.png)

*   Select the filters of your choice. Our app enables you to download payslips based on the portal status, work location and designation

The link to initiate download will be generated and you will be notified once it is ready.

![Create Pay Run](/payroll/help/en-om/payruns/download-payslip-filter.png)

To download the file, click **More** > **Show Downloads** > **Download** and choose a location to store the documents.

![Create Pay Run](/payroll/help/en-om/payruns/show-downloads.png)

If you make any changes to the pay run after you download these documents, the existing link will expire and you will not be able to use it. You need to re-initiate the file generation and then download the modified pay run details.

* * *

## New Joinee Arrears

New Joinee Arrear is the amount the employee has earned but has not yet been paid because they joined the company right after the pay run has been processed for a given pay period.

When the employer marks an employee as a New Joinee, our app calculates the arrears using the employee’s date of joining and the company’s pay period.  Our app takes into account the number of days a new employee has worked and calculates their salary or wages accordingly. This amount is then added to the first regular payroll of the new employee.

For example, if an employee joins a company on the 15th of the month, and the pay period is from the 1st to the 30th of the month, our app will calculate the salary for the 15th to the 30th of the month as a new joinee arrear and add it to the first regular of the new employee.

**Processing New Joinee Arrears in our app**

When a new employee joins the organization, their compensation package might take time to finalise. The HR or payroll administrator can update this information in our app to calculate the correct salary and track the arrears.

You can select employees who have new joinee arrears while:

1.  Creating or editing an employee
2.  Processing the pay run for an employee

To process new joinee arrears when you are adding a new employee or editing an employee,

*   Click **Employees** on the left sidebar.
*   Click **Add Employee** in the top right corner or **edit** an existing employee.
*   Select the **Pay as arrears in the upcoming pay run** option.
*   Complete the employee profile and click **Save.**

![Create Pay Run](/payroll/help/en-om/payruns/employee-arrear.png)

While processing payroll, the administrator can check if any employees have new joinee arrears. The arrears will then be processed along with the the employee’s first pay run.

To process new joinee arrears when you are processing the pay run for an employee ,

*   Click **Pay Runs** on the _left sidebar_.
*   Click **View Details** next to the pay run you are processing.
*   Click the **More** icon next to the employee for whom you are trying to process the new joinee arrear and select **Skip from this payroll**.

![Create Pay Run](/payroll/help/en-om/payruns/employee-arrear-skip.png)

*   Select **Pay as arrears in the next pay run.**
*   Enter the reason for skipping the employee.
*   Click **Proceed.**

![Create Pay Run](/payroll/help/en-om/payruns/payrun-arrear.png)

**Pro Tip:** If there is an employee in a pay run for whom you don’t want to make a payment, you can exclude them from the current pay run and instead include their payment as arrears in the next pay run.

The employee will be skipped for the current pay run and the arrears will be processed in the upcoming pay period.

**Pro Tip:** If you’ve skipped a new joinee arrear it can be reverted by adding the skipped employee to the payroll.

### Import New Joinee Arrear Details

You can import the new joinee arrear details if you have to add themin bulk.

Here’s how you can import them:

*   Click **Employees** on the left sidebar.
*   Click the **More** icon in the top right corner and click **Import Employees**.
*   Select **Employee Basic Details** or **Employee Details** as the import type.
*   Upload the file containing the details in the format prescribed below.

![New Joinee Arrears](/in/payroll/help/images/pay-runs/import-new-joinee-arrears.png)

*   Select how you want to handle duplicate entries.
*   Map the import file fields with the fields in our app and click **Import.**

* * *

## LOP Reversal

The process of reversing the Loss of Pay (LOP) deduction for an employee is referred to as LOP Reversal.

**What is LOP?**

LOP is deduction from an employee’s salary in case they are absent from work without prior approval or if they’ve exhausted their paid leaves.

**How does LOP Reversal work?**

When an employee takes unapproved leaves, you can apply the corresponding LOP deduction in the app. However, if the employee later provides a valid reason for their absence, you can reverse the LOP deduction in the upcoming months.

Here are three use cases for LOP reversal:

1.  **The employee’s absence was due to taking approved leave, which was granted after the unpaid leave of absence (LOP) was applied.** If the leave is approved, the LOP can be reversed.
    
2.  **The cause for the employee’s absence was medical:** A worker might have missed work because of an illness or another medical issue that was not previously covered by paid leave. The LOP deduction can be reversed if the employee subsequently submits medical certifications or other acceptable proof.
    
3.  **Oversight** **in payroll calculation:** In some cases, the LOP deduction may have been made in error due to an oversight in payroll processing. If this is identified and corrected, the LOP reversal process can be initiated to ensure that the employee is paid the correct salary amount.
    

Overall, LOP reversal helps ensure that employees are paid accurately and fairly. It helps to avoid unnecessary deductions and promotes transparency and efficiency in payroll processing.

### Reversing LOP

Here’s how you can reverse LOP:

*   Go to _Pay Runs_ on the left sidebar.
*   Click **View Details** next to the current Regular pay run.
*   Select the employee for whom you want to reverse the LOP of a previous month. 

**Pro Tip:** Click the dropdown below Employee Summary and select **Employees with LOP** to filter employees with LOP.

*   Click the dropdown next to **Add LOP** and select **Adjust Past LOP.**

![Create Pay Run](/payroll/help/en-om/payruns/adjust-past-lop.png)

*   Select the month for which you want to reverse or correct the LOP.
*   Enter the number of days for which you want to reverse or correct the LOP.

![Create Pay Run](/payroll/help/en-om/payruns/lop-reversal-details.png)

**Insight:** The maximum number of days you can reverse is based on the LOP applied during that particular month.

*   Click **Save.**

The LOP will be reversed, and the employee will be compensated in the current payroll.

**Pro Tip:** The LOP deducted in the past fiscal year can be reversed only at once along with the January pay run of the current financial year, whereas the deduction of LOP in a single pay run can be reversed over several months.

By following the above steps, you can quickly and easily reverse LOP deductions and ensure your payroll processing is transparent and efficient.

### Import LOP Reversal Details

You can also import the LOP reversal details of employees in the Pay Run module. This feature will come in handy if you have to add LOP Reversal details in bulk. Here’s how you can import them:

*   Click **Pay Run** on the left sidebar.
*   Click **Import/Export** in the right side of the screen and select **LOP Reversal**.
*   Upload the file containing the details in the format prescribed below:

![LOP Reversal](/in/payroll/help/images/pay-runs/lop-reversal-import-details.png)

*   Select how you want to handle duplicate entries.
*   Map the import file fields with the fields and click **Import.**

The file will be imported and the LOP reversal details will be mapped against each employee.

* * *

## Resettlement Payroll

**Note:** This feature is only available in early access. Contact [support@zohopayroll.com](mailto:support@zohopayroll.com) to get access for your organisation.

In certain situations, employees may be terminated from their positions without receiving their due compensation. With the Resettlement Payroll feature, you can efficiently process payroll for terminated employees who were not compensated at the time of termination.

This feature ensures that such payments are separated from the regular payroll. You can easily include the terminated employees in the Resettlement Payroll.

**Scenario:** Zylker, an organisation with 500 employees, recently went through a restructuring process. This led to the termination of several employees. Due to the complexities involved, these employees did not receive their final compensation when they left. Ahmed, the head of payroll at Zylker, can use the Resettlement Payroll feature to efficiently process the pending payments for these terminated employees in a single go.

### Initiate a Resettlement Payroll

To initiate a resettlement payroll for your terminated employees:

1.  Click **Pay Runs** on the left sidebar.
2.  Click **Create Pay Run** in the top right corner and select **Resettlement Payroll**.  
    ![Create a New Resettlement Payroll](/payroll/help/ae/payruns/resettlement-payroll/create-resettlement-payroll.png)
3.  In the popup that appears, select the payment date for the exited employees.  
    ![Select the Paydate for Resettlement Payroll](/payroll/help/ae/payruns/resettlement-payroll/paydate-for-resettlement-payroll.png)
4.  Click **Save**. You’ll be redirected to the _Add Resettlement Details_ page, where all terminated employees will be listed.  
    ![Add Resettlement Details Page](/payroll/help/ae/payruns/resettlement-payroll/add-resettlement-details-page.png)

### Add Earnings and Deductions

To add earnings and deductions for the eligible employees:

1.  In the _Add Resettlement Details_ page, click **Add Earnings / Deductions** for an employee.  
    ![Add Earnings and Deductions for Resettlement Payroll](/payroll/help/ae/payruns/resettlement-payroll/add-earnings-deduction-for-resettlement-payroll.png)
2.  Enter the earning and deduction amounts applicable for the particular employee.  
    ![Add Earnings and Deductions Applicable for Employee](/payroll/help/ae/payruns/resettlement-payroll/add-earnings-deduction-for-employees.png)

**Insight:**

*   Under Earnings, you can add Bonus, Commission, Leave Encashment, and Gratuity.
*   Under Deductions, you can add Salary Advance and Fines and Damages.

3.  Click **Save**.

The Resettlement Payroll will be created in Draft status.

**Pro Tip:** If you initiate exit processes for employees, they won’t be included in Resettlement Payrolls that are in Draft status. You can add these newly terminated employees by clicking Add Employees on the Resettlement Payroll page.

Once you have added the necessary details, you can approve the Resettlement Payroll and proceed with making the payments to your employees.

* * *

## Download Bank Advice and Wage Files

Once you approve the payroll, the Bank Advice and Wage files will be available for download.

### Download Wage File

*   Navigate to the payroll summary page and select **Download Wage File**.
*   Select whether to include employees based on the status of their salary payments:
    *   **Unpaid**: Choose this option to include only those employees who have not yet received their salaries. This is helpful for generating Wage files in anticipation of upcoming payments.
    *   **Both (Paid & Unpaid)**: This option includes all employees in the Wage file, regardless of whether they have been paid or not.
*   You can also futher filter for whom you want generate Wage file for based on the below criteria.
    *   **Department**: Select a specific department if you need to generate the Wage file for a particular segment of your organization.
    *   **Designation**: Filter the Wage by job designation to target specific roles or levels within the company.
    *   **Add a Tag**: Use this option to filter employees based on custom reporting tags that you’ve applied within your organization. Tags allow you to create tailored reports that meet specific internal or regulatory requirements.
*   Select **Disbursement Account** number from which the payroll funds will be released. This account is usually tied to your company’s primary bank account and is required to ensure the correct processing of salary payments. This field is mandatory.
*   Select the work location for which the Wage file is being generated.
*   Choose the required format for the Wage file. The format you select should comply with the regulatory requirements or the specific needs of the financial institution to which the file will be submitted.
*   Select the file format for the download.
*   Once all the necessary information has been entered and the appropriate filters and options have been set, click the **Save & Download**.

![Create Pay Run](/payroll/help/en-om/payruns/download-wage-file.png)

This will generate the Wage file and save it to your device, ready for submission to the relevant financial institutions or regulatory bodies.

### Download Bank Advice

*   On the payroll summary page, click the **Download Bank Advice** option.
*   You can filter for whom you want generate bank advices for based on the below criteria:
    *   **Department**: Use this field to select a particular department. This is helpful if you want to generate a Bank Advice file for employees from a specific department, such as HR, Finance, or Sales. If you wish to include all employees across departments, leave it set to “All Departments.”
    *   **Designation**: This filter lets you select employees based on their job titles or roles within the company. For instance, you might want to generate advice only for managers or executives. Leaving this field set to “All Designations” will include employees of all roles in the file.
    *   **Add a Tag**: This option allows you to apply custom tags to further categorize or filter the employees. Tags can be used for a variety of purposes, such as identifying custom groupings within your organization.
*   Select the **Bank Statement Format** in which the bank statement will be generated. The format might vary depending on your bank’s requirements or the standard practice in your region.
*   Choose the file format for downloading the Bank Advice.
*   If you want to add an extra layer of security to the Bank Advice file, check the **Protect this file with a password** box to enable password protection. You will be prompted to set a password, which will be required to open the file. This is especially useful for files containing sensitive employee salary information.
*   After configuring all settings and filters, click **Download** to generate and save the Bank Advice file to your computer. The file will be ready for submission to your bank or for internal use, depending on your needs.

![Create Pay Run](/payroll/help/en-sa/payruns/download-bank-advice.png)