Zoho Payroll for Indian businesses in India means Zoho Payroll India setup guide contributions, ESI deductions, Professional Tax, TDS on salary, and compliance with multiple statutory bodies. Zoho Payroll handles all of these within a single payroll run, reducing calculation errors and missed filings.

Statutory payroll calculations in Zoho Payroll

Statutory Components

ComponentEmployeeEmployerAuthority
EPF12% of basic12% of basicEPFO
ESI0.75% of gross3.25% of grossESIC
Professional TaxVaries by stateN/AState govt
TDS on SalaryAs per slabN/AIncome Tax

Setting Up PF

Enter your PF establishment code in Settings > Statutory Components > PF. Choose whether PF is on Rs. 15,000 ceiling or actual basic. Zoho Payroll computes both employee and employer shares on every payroll run.

Getting this right matters, because a misconfigured PF setup tends to surface later as short-deductions, penalties, or employee disputes at year-end. The standard deduction is 12% of basic salary from the employee, matched by 12% from the employer, though the employer’s share is split across EPF, EPS, and EDLI rather than credited to the employee’s PF account in full.

ESI Configuration

ESI applies to employees with gross up to Rs. 21,000/month. Enter your ESIC code. Zoho Payroll auto-discontinues ESI when salary crosses the threshold.

ESI is enabled per employee automatically based on their gross salary, so no manual toggling is required from one payroll run to the next.

PF and ESI remittance challan preparation

Professional Tax

Pre-configured slabs for all states that levy PT (Maharashtra, Karnataka, Tamil Nadu, etc.). Set your state and Zoho Payroll applies the correct slab per employee.

To configure this, go to Settings > Professional Tax and select your state. Beyond Maharashtra, Karnataka, and Tamil Nadu, West Bengal and Telangana are among the other states that levy PT, and Zoho Payroll ships with pre-configured slabs for each. For employees based in states that do not levy PT, no deduction is made.

TDS on Salary

Employees submit investment declarations at the start of the financial year. Zoho Payroll distributes projected tax across months. Update with actual proofs in January-February and the system recalculates remaining TDS.

Zoho Payroll generates payslips automatically once payroll is processed for the month, showing gross salary, all deductions (PF, ESI, PT, TDS), and net take-home pay. Employees can access their payslips through the Zoho Payroll self-service portal, or through the Zoho People mobile app if your organisation also uses Zoho People for HR.

TDS on salary (Section 192) is calculated based on the investment declarations employees submit through the employee portal in April, along with proofs such as HRA, LTA, 80C, and 80D. Zoho Payroll projects the employee’s annual income, applies the applicable tax slab, and distributes the TDS liability evenly across the remaining months of the year. When actual proofs come in, the system recalculates the final 2 to 3 months’ deductions to match. Zoho Payroll also generates Form 16 at year-end for each employee, which they need for their individual ITR filing.

Filing and Remittance

After each payroll run, Zoho Payroll generates challan reports for PF (due 15th), ESI (due 15th), and TDS (due 7th). It also generates ECR files for direct upload to the EPFO Unified Portal.

The monthly compliance routine breaks down into four steps: run payroll (confirming attendance and variable pay), review and approve the payroll run, generate and pay the statutory challans (PF, ESI, PT, TDS), and file the returns (ECR for PF, the ESI return, and the TDS quarterly return). Zoho Payroll generates the challan amounts and the ECR file, but payment and filing still happen on the respective government portals, principally the EPFO Unified Portal, the ESIC portal, and TRACES for TDS.

Payroll data connects to Zoho Books for statutory payment challan entry and reconciliation. The Zoho Books complete setup guide for Indian businesses covers the chart of accounts structure that works alongside Zoho Payroll for clean P&L reporting.

Frequently Asked Questions

Does Zoho Payroll generate PF ECR files?
Yes. Download the ECR file and upload directly to the EPFO Unified Portal. No manual ECR preparation needed.
Can it handle different PT rates for employees in different states?
Yes. Zoho Payroll supports multi-state payroll. Each employee is assigned a work location, and the professional tax rate for that state applies to their salary. If your company has offices in Maharashtra and Karnataka, employees at each location will have the correct state-specific PT deducted automatically.
New tax regime vs old?
Each employee selects their regime. Zoho Payroll handles both in the same payroll run for different employees.
Code on Wages 2019 compliance?
Zoho Payroll is prepared for the changes. When rules are officially enforced, the system will update PF and gratuity calculations accordingly.
Does Zoho Payroll handle payroll for contract employees or freelancers?
Zoho Payroll is designed for full-time employees on the payroll. Contract workers paid via purchase orders or service agreements are typically handled through Zoho Books as vendor payments with TDS under Section 194C or 194J. Contract employees on fixed-term employment contracts can be added to Zoho Payroll as regular employees with a defined tenure.
How does Zoho Payroll handle salary revisions mid-year?
When you update an employee’s salary in Zoho Payroll, you set the effective date for the revision. Zoho Payroll recalculates PF, ESI (if applicable), and TDS projections from that date forward. If the revision is backdated, Zoho Payroll calculates the arrears due and can pay them as a separate arrears component in the next payroll run.