Zoho Books with Zoho Payroll

Keeping track of the salaries you pay your employees is as important as paying them on time. You will have to record the wages you pay and the taxes you deposit in your Zoho Books organisation. Posting manual entries after every pay run could be time-consuming and demanding.

This is where Zoho Payroll comes to the rescue. Zoho Payroll is a complete payroll management solution which automatically calculates salaries, taxes, deductions, sends out payslips and performs all other payroll related activities.

It comes integrated with Zoho Books so your payroll and accounting is in sync. All payroll expenses and tax liabilities will be recorded in their respective Expense and Liability accounts. This will then reflect in your Profit and Loss report so your financial statement is accurate.

Note: This document is applicable only for users in the India edition of Zoho Books.

Set up Zoho Payroll

If you are new to Zoho Payroll, you can easily set up your organisation and get started.

Try Payroll Set Up

Once you’ve finished configuring all the salary components, click Finish Setup.

Configure Accounts

Once you’ve set up your payroll, you can configure the accounts with which the accounts in which you want the payroll transactions to be recorded in. For instance, you can either choose to track all statutory deductions under a single account, or track EPF, ESI and PT under different accounts. You can also create sub-accounts to track them based on your requirements.

To do this:

Edit Configure Books Map Accounts

Functions in Zoho Payroll

Here are some of the key functions you will be able to perfom with your Zoho Payroll organisation:

Note: If you are using the Standard Plan of Zoho Books, you will have access only to the free version of Zoho Payroll, by default.

Add Employees

The Employees module in Zoho Payroll allows you to add and manage employees’ personal and salary details, assign deductions to them, upload their IT Declaration and so much more.

To add an employee in Zoho Payroll,

Add Employee

Once you’ve added your employees, you can also add pre-tax deductions, post-tax deductions, add perquisites, revise salary and submit IT Declaration and POI on your employees’ behalf. Learn more about managing employees.

Note: Based on your Zoho Books plan, you will be able to manage either 10 or 20 employees.

Set up Statutory Components

These are components defined under certain enactments passed by government bodies like Employee Provident Fund Organisation (EPFO). Contributions are made by employees and employers towards the employees’ long term financial and social well-being. There are 4 main statutory components in India. Learn the guidelines and how to set up each of them in Zoho Payroll:

Process 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 configure the payroll structure for your company and process pay runs for your employees effectively. To do this:


The following page displays all the key information related to the pay run such as Payroll Cost, Payday, Net Pay, Taxes & Deductions Summary and Employee Summary. Learn more about processing pay runs.

Create Salary Templates

Create templates for commonly used salary structures and save time and effort. Instead of manually entering the salary details for employees having the same salary structure, you can create a common salary template and assign them to employees. To create a salary template:

Salary Template

Learn more about salary templates.

Direct Deposit of Salaries

Once you generate pay runs, you will be able to deposit salaries directly from Zoho Payroll to your employees’ accounts. The payment will be initiated for the Direct Deposit enabled employees and if you have integrated your organisation with ICICI Bank. To make payments:

Initiate Payment

Learn more about the ICICI Bank integration and direct deposit of salaries.

Employee Portal

Employee Portal allows your employees to view their salary details and perform all payroll related activities like declaring FBP and IT, submitting investment proofs and creating reimbursement claims. Once your employee accepts the invitation, they would have to set up their portal account.


Learn more about accessing the employee portal.

Not just this, you can head over to the Zoho Payroll’s help guide to view all the available features.

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