Best Payroll Software for Startups in India: GreytHR vs Zoho vs RazorpayX

01What Payroll Software Must Do in India

Payroll software in India is a tool that calculates salaries, applies statutory deductions, pays the right amounts to the government, and produces payslips and returns, all with an audit trail. Indian payroll is not just “salary minus tax”; it bundles several statutory items that each have their own rules and deadlines.

Before you compare brands, get clear on what any tool must handle for you. A startup payroll system should cover these five things end to end:

• Provident Fund (PF / EPF): compute employee and employer contributions and generate the monthly ECR challan. EPF becomes mandatory at 20 employees.
• Employees’ State Insurance (ESI): compute and file ESI for employees with wages up to ₹21,000 a month. ESI becomes mandatory at 10 employees.
• Professional Tax (PT): deduct and pay PT, which is state-specific (it exists only in some states, for example Maharashtra, Karnataka and West Bengal).
• TDS on salary: compute tax under the old or new regime, deposit it, and generate Form 24Q and Form 16.
• Payslips, leave, attendance and reports: issue compliant payslips and keep records you can hand to an auditor or investor in due diligence.

02The 5 Payroll Tools Indian Founders Shortlist

Five names cover almost every startup shortlist in India. Here is what each one is, in one line, and who it suits, before we put numbers against them.

1GreytHR

A compliance-first HR and payroll platform built specifically for India, used by tens of thousands of companies. It handles PF, ESI, PT and TDS across multiple states with strong statutory reporting, plus leave and attendance. Best for: teams of roughly 10 to 200 plus, especially multi-state, that want depth over simplicity.

2Zoho Payroll

Clean, affordable payroll from the Zoho stable, with tight links to Zoho Books and Zoho People. It covers PF, ESI, PT and TDS and is genuinely easy to set up. Best for: small growing teams that want simple, low-cost payroll, especially if they already use Zoho for accounting or HR.

3RazorpayX Payroll

Payroll built around payments: it disburses salaries and pays PF, ESI, PT and TDS directly from your RazorpayX account, in one flow. It has a free or very low-cost tier for small teams. Best for: early startups that want salary payouts and compliance payments automated together.

4Keka

A full HR plus payroll suite with a strong employee experience, analytics and performance modules. Payroll covers all the Indian statutory items. Best for: scaling teams of roughly 50 to 500 that want HR and payroll in one polished platform.

5Kredily

A free-forever HR and payroll tool that covers the basics, with paid add-ons. Best for: very early, cost-sensitive startups that just need to run a handful of salaries correctly before they can justify a paid tool.

03Best Payroll Software in India: Comparison Table

Here is the side-by-side view. Prices are indicative guide ranges for India as of 2026 and change often, so verify current pricing on each vendor’s site. Most paid plans charge per employee per month with a monthly minimum.

04Best Payroll Software for a Small Team (Under ~25)

For a small startup team, the best payroll software is the cheapest tool that still gets PF, ESI, PT and TDS right. You do not need an HR suite yet; you need correct payslips and on-time filings.

When Brewly made its first 6 hires, two options fit well. RazorpayX Payroll made sense because the founders already banked with RazorpayX, so salary payouts and PF, ESI, PT and TDS payments flowed from one place on a free or near-free tier. Zoho Payroll was the alternative, attractive because Brewly kept its books in Zoho Books, so payroll entries reconciled automatically. Kredily is the fallback when budget is zero and needs are basic.

05Best Payroll Software for a Larger Team (25 to 500)

Once you cross roughly 25 employees, or operate across multiple states, compliance depth matters more than price. This is where GreytHR and Keka pull ahead of the simpler tools.

By the time Brewly reached 40 people across two states, Professional Tax rules differed by state, ESI and PF filings grew heavier, and the team needed structured leave and attendance. GreytHR became the natural choice for its compliance depth and multi-state statutory reporting. A company that also wanted performance reviews, onboarding and richer HR analytics in the same platform would lean toward Keka instead. Both cost more per employee than the small-team options, but at this size the cost of a missed or wrong filing is far higher than the subscription.

06Setting Payroll Up Correctly After Incorporation

Choosing a tool is only half the job. To run payroll legally in India you also need the right registrations in place, and these often get missed right after incorporation. Sort these before your first salary run.

• PAN and TAN for the company (TAN is needed to deposit TDS; SPICe+ issues both at incorporation).
• EPFO and ESIC registration: SPICe+ bundles these via AGILE-PRO-S (INC-35) at incorporation, so most new companies already have them.
• Professional Tax registration where applicable: PTEC for the company and PTRC for employees, in PT states.
• Company bank account for salary disbursal, plus the paid-up capital deposited so you can actually run payroll.
• Employee details: PAN, Aadhaar, bank account and UAN for PF, captured cleanly in the payroll tool.

For non-resident founders this rarely changes payroll itself, but a non-resident director still needs an Indian PAN, and if any payroll-related KYC documents come from abroad they may need to be apostilled or notarized, which adds time. Grab our free document checklist and post-incorporation compliance checklist so nothing slips between registration and your first payday.

07Founder Watch-Outs Before You Pay the First Salary

The tool rarely fails; the setup does. These are the mistakes that turn cheap payroll into expensive penalties.

A spreadsheet has no PF logic, no PT-by-state table and no audit trail. Switch the moment you have a salaried employee. Even a free tool is safer than manual maths.

Hiring your first employee in a new PT state creates a fresh registration and filing obligation. Confirm your software supports that state before payday, or you will quietly accrue PT defaults.

Contractors are paid through accounts payable with TDS under section 194C or 194J, not through payroll with PF and ESI. Mixing the two creates wrong deductions and a due-diligence flag. Keep payroll for employees and pay contractors separately.

Payroll should not depend on one person’s login. Give your accountant or controller access, document the cycle, and make sure salaries and filings run even when the founder is travelling.

08Frequently Asked Questions