So you have a growing small business in India with a bunch of moving parts and people to pay. An accounting team (or maybe just you) tracking salaries and taxes, an HR team managing sensitive employee information, managers handling attendance and leave, and compliance requirements in our loved tool – Excel.
You could rely on Excel sheets to handle payroll, but keeping everything accurate and compliant sounds like spreadsheets are an expensive, inefficient way that can easily create silos and stress. A better solution is dedicated payroll software built for small businesses in India.
We did in-depth research on payroll software, spoke to HRs who are actually running payroll month after month, and watched so many demos that we started to dream in payslips and compliance dashboards. Based on all that, we condensed down a list of the 15 best payroll software in India for small businesses so that you don’t have to spend hours and days choosing one.
The Best Payroll Software in India for Small Businesses at Glance
- NYGGS Payroll for the best all-around HR software with a payroll module
- Keka – an excellent HR software with a payroll management solution
- greytHR is great for its statutory compliance feature
- Zimyo claims that payroll can be processed in just 5 clicks
- Quikchex for full control and simplicity in payroll management
- RazorpayX Payroll for freelance, project-based and contractor pay management
- Kredily comes with a free plan with limited functionality
- Pocket HRMS for end-to-end payroll automation with its own smHRt Payroll engine
- SumHR – known for great support and commendable uptime
- Superworks payroll software is the best option for quicker salary disbursement
- Zoho Payroll – best for small businesses who are already using Zoho’s tools
- Darwinbox is the best choice if you want a multi-state labour law-compliant tool
- HROne for multi-country payroll compliances
- FactorHR Payroll is best for companies looking for GPS-based attendance integrated with payroll
- Qandle is the best payroll software for its reporting and analytics features
All-Around, Best Payroll Software in India for Small Businesses
1. NYGGS Payroll
Most payroll software is built for offices. NYGGS goes beyond that. It’s built for offices as well as heavy industries like construction, manufacturing and mining. NYGGS payroll has enterprise-grade features, modules and security and comes with the entire HRMS software ecosystem, yet comes with an affordable pricing structure. With its power of AI, where project-linked pay, set & forget salary structures, and statutory compliances like PF, TDS, LWF, and gratuity are all impressive features. Besides that, it comes with a minimalist dashboard, multiple filters for easy access, and downloadable reports about payroll history and trends that keep HR and payroll teams always updated.
Reasons it is in this list:
- PF, PT, TDS, and ESIC compliance modules
- Automated salary & benefit deductions
- Loan, advance, and EMI tracking
- Built-in AI chatbot for support
2. Keka
Keka doesn’t just calculate payroll—it orchestrates it. When you Google “the best payroll software in India”, most probably you will find it on the first page. This is because Keka is one of the leading HRMS software providers in India. With audit-ready reports, multi-entity compliance, and deep ERP integrations, it handles everything from arrears to scenario planning at enterprise scale.
Reasons it is in this list:
- Trusted by 10,000+ companies
- Handles 10–10,000 employees seamlessly
- Pre-built integrations (Tally, SAP, QuickBooks, Zoho)
- Multi-entity payroll with scenario planning and forecasting
3. greytHR
greytHR has been around longer than most payroll startups combined — and it shows. With 23,000+ clients, it’s battle-tested for Indian compliance, accurate disbursements, and real-time reporting. Its UI stands out among others – easy, engaging and minimalist.
Reasons it is in this list:
- Used by 23,000+ companies in 250+ cities
- 100% statutory compliance
- PayNow for instant salary transfers
- The ESS portal is reducing admin work by 80%
4. Zimyo
Payroll errors kill employee trust. Zimyo solves that with a clean, 5-click payroll process that syncs directly with attendance, leave, and biometric data. No delays. No mismatched numbers. Just accuracy.
Reasons it is in this list:
- Payroll in just 5 clicks
- Built-in attendance and biometric integration
- Automated PF, ESIC, and TDS filings
- Custom workflows and access control
5. Quikchex
Quikchex is for HR managers who crave control and simplicity. From loan management to flexi-benefits, everything runs through one connected system that drastically cuts payroll time from 7 days to just 1 day. Additionally, this best payroll software in India supports diverse compensation models, includes no complex features, offers auto-generated bank reports for disbursements, as well as provides reconciliation support.
Reasons it is in this list:
- Custom salary templates and flexi-benefit design
- Automated tax, PF, and ESIC compliance
- GPS-based attendance integration
- Loan management and auto-deductions
- Custom payslip templates with company branding
Low-Price Payroll Software for Small Business in India
6. RazorpayX Payroll
RazorpayX Payroll brings fintech precision to HR. It is undoubtedly the best payroll software in India for small businesses that have to pay freelancers, remote staff, and contractors in one dashboard — while automating tax filing and compliance.
Reasons it is in this list:
- Pay full-time, contract, and freelance employees.
- One-click compliance filing (TDS, PF, PT, ESIC)
- Real-time alerts for regulatory changes
- 45+ HRMS & attendance integrations
7. Kredily
Most startups delay payroll automation, thinking they’re “too small” for it. However, Kredily flips that logic. It’s a free, cloud-based payroll software that automates everything—from salary slips to PF filings—so you can stay compliant and pay your team on time, every time.
Reasons it is in this list:
- Free forever plan with 15-minute activation
- Integrated compliance features (PF, TDS, ESI, PT)
- Overtime, variable, and performance-based bonus payouts
- AI-powered “Magic Upload” for instant data import
8. Pocket HRMS
Imagine payroll that fixes its own errors. Pocket HRMS does that. Its smHRt Payroll engine uses machine learning to catch mistakes before they happen — while keeping your data safe on Microsoft Azure’s encrypted cloud.
Reasons it is in this list:
- Machine Learning–powered “smHRt Payroll” for error detection
- Hosted on Microsoft Azure (256-bit encryption)
- Timesheet and project integration
- Multi-schedule payroll (hourly, contract, full-time)
9. SumHR
SumHR is cloud-based payroll software that brings automation, flexibility, and accuracy together. Moreover, it handles everything from payroll calculation and TDS to leave deductions, arrears, and full-and-final settlements.
Reasons it is in this list:
- Cloud-based, stress-free payroll
- Unlimited salary components
- Proof-submission workflow for tax declarations
- Full & final settlement automation
10. Superworks
Unlike traditional tools, Superworks believes payroll shouldn’t take hours — or even half an hour. With its AI-driven Super Payroll, you can process salaries, bonuses, and advances in just four clicks. Fast, automated, and scalable — exactly what growing startups need.
Reasons it is in this list:
- 4-click salary disbursement
- AI-powered Super Payroll for automation
- Loan, bonus, and advance management built-in
- 60,000+ active users across 15+ industries
Best Payroll Software in India for Small Businesses with Global Compliances
11. Zoho Payroll
Zoho Payroll feels like a payroll built for precision. It scales effortlessly, automates compliance in 28 states, and integrates with Zoho’s entire ecosystem — making it a no-brainer for teams already using Zoho Books or People. This is the best payroll software in India for companies using Zoho Books, People, or CRM already.
Reasons it is in this list:
- 40+ real-time reports and multi-level approvals
- 21 comprehensive payroll and compliance features
- Native integration with the Zoho suite and external ERPs
- PF, ESI, LWF, and IT compliance across 28 states
12. Darwinbox
Our research identified Darwinbox as a full enterprise HRMS engine but also has affordable plans for small businesses. And its payroll module is commendable. With real-time data sync, multi-currency support, and Gartner recognition, it handles complex, multi-country payroll like a pro.
Reasons it is in this list:
- 100% digitised, audit-ready payroll
- Multi-country & multi-currency support
- Unified HR + payroll + finance platform
- Recognised in Gartner’s Magic Quadrant (2025)
13. HROne
When you’re running payroll across 40+ locations, spreadsheets won’t cut it. HROne brings AI, analytics, and automation together to simplify compliance-heavy, multi-state payroll operations. Its name also suggests that HROne provides software for automating the entire HRMS ecosystem, not just payroll.
Reasons it is in this list:
- Multi-state compliance across 40+ locations
- AI-powered voice assistant for HR operations
- Deep ERP integrations (SAP, Oracle, Tally)
- 3D payroll analytics & salary comparison reports
14. factoHR Payroll
factoHR is what happens when payroll meets mobility. This is the best payroll software in India for small businesses who need GPS-based attendance, mobile ESS, and bilingual payslips features.
Reasons it is in this list:
- GPS-based attendance integrated with payroll
- Mobile ESS for pay and tax visibility
- Tax regime selection (old/new) with projections
- Payslips in vernacular language
15. Qandle
Payroll for 20 people is easy. Payroll for 200? Not so much. Qandle scales beautifully in that middle ground. It automates compliance, deductions, and disbursements without overwhelming payroll teams. Plus, its reporting & analytics tools are so powerful that you have all the payroll information visually presented and readily available to export.
Reasons it is in this list:
- Handles 10 to 10,000 employees
- Automated compliance (PF, ESI, LWF, PT)
- Direct bank transfer integration
- 80% admin workload reduction via ESS
Why NYGGS Is the Best Payroll Software in India for Small Businesses
Each tool mentioned above has its own benefits, but there is one payroll software that can handle it all, from payroll to team management and end-to-end HR operations. That standout tool is no doubt NYGGS, which comes integrated with smart automation features that are hard to match.
With years of experience in managing comprehensive HR and payroll requirements, this payroll software is used to process payroll at scale, ensuring on-time, accurate, and transparent salary processing across industries.
It has a large user base with over 20,000 employees spread across multiple states of India and business verticals. The experience gained throughout the journey of implementation on such a diverse workforce made NYGGS solution the best payroll software in India for small businesses.
Before NYGGS, the payroll team was spending 30+ hours on implementation and processing cycles. Post-deployment? That number dropped to just 1.30 to 2 hours. That’s a 95% reduction in payroll implementation time – all this without sacrificing compliance, accuracy, or employee experience.
Book a demo to learn more!