Top 10 Best Payroll Software For SMEs In India

Payroll is the process of dispersing salaries to employees in a timely and orderly manner. But payroll is not just limited to payments of salaries but a complex process, right from creating payroll policies and CTC structures to depositing dues like PF, ESCI, and other compliance filings with the respective authorities. Companies with an inefficient payroll process run the risk of dispersing delayed and inaccurate salaries, legal issues, and hampering overall productivity due to employee dissatisfaction. Before checking out the best payroll software in the market, let us understand what pointers are essential to consider.

Can a Small Company Run Its Payroll Manually?

Although Indian payroll is complex, many companies run their payroll in-house through excel or some other accounting tool. A growing startup with a team of 10 to 20 members can run its payroll using the methods mentioned above but may still need payroll experts to get all the calculations and deductions right and this comes at a heavy cost. Hence running payroll manually is not scalable and susceptible to human errors.

Here are some concerning facts and figures about payroll processing

1. 25% of small businesses use pen and paper to track finances, and 45% don’t have their own accountant or bookkeeper (Source: Clutch)

2. 49% of workers will start a new job search after experiencing only two problems with their paycheck (Source: The workforce institution of Kronos)

3. Non-submission of income tax returns as required under section 139, subsection (1) of the Income Tax Act can result in a penalty of Rs5000 or more. (Source: TOI Business)

Watch out for these specifics before you choose the best payroll software for you.

1. Is the payroll software compatible with your payroll policies?

Policies and payroll components differ from organization to organization. You may require a tool just for basic and variable calculations of your employees or you may be looking for a comprehensive system that can be customizable according to your complex payroll policy workflows. We highly recommend that you verify whether your payroll software can cater to all your requirements effectively to avoid any manual interventions thereafter.

2. What features/modules do they offer?

Most payroll software has all the standard features like automated payroll calculations, Tax deductions, Mobile access or Employee Self Service Portal, Expense Management, Allowances, and Reimbursements to name a few. But a detailed evaluation is needed to understand some more niche features like Flexi benefits, Investment declarations and verifications, multiple CTC structures, and the ability to run batch-wise payroll which is suited for organizations that have complex requirements.

3. Can the software manage all statutory compliance calculations?

According to government research, around 21% of HR and Payroll Managers find it difficult to stay afloat in filing PF, ESCI, LWFM, and other labour compliances accurately. Failure in filing all necessary compliances can lead to legal risk and hefty fines to be paid. To ensure a safeguard from these problems, you need to make sure that your payroll software can process all compliance-related calculations and provide you with a team of compliance experts to do all necessary filings can be considered a huge plus.

4. Can it generate all types of payslips and reports?

Payroll reports are one of the most important aspects of a Payroll Solution. They are crucial for compliance filings, tax calculations & verifications and also can be used for presentations. Having a checklist for all payroll reports and the ability to create custom reports is important. The most important step after payroll is the generation of payslips and your Payroll software should be able to automatically create all standard, tax, and FNF payslips. The process of accessing payslips for employees must be a user-friendly process as well.

5. What does the implementation process look like?

Even the best payroll software vendors may take anywhere between 3 days to a week to implement their system in your organization. Decision-makers must understand the implementation process and data migration requirements before finalizing the software. We would recommend you request a test run with your payroll software vendor to test the feasibility of the tool before using the solution at full capacity.

6. What is your budget?

Payroll software range in price from Rs 50/- per employee per month to Rs.300/+ – per employee per month (usually with a base floor rate). Your requirements and employee strength will be one of the most important factors in determining the budget for your next Payroll Software.

7. Is the customer service reliable?

Having a highly responsive and proactive after-sales service is essential for any HR and payroll software. An account manager with an ‘on demand’ direct phone call access comes in handy more often than you might think. Dedicated account managers assist you with any inquiry or issues that require immediate attention.

8. Is your data secure on the software?

Data security is more important now than ever. Your payroll software will contain sensitive information about your company and employees’ salary info in form of official documents stored by the payroll team. Any compromise with the integrity of this data can lead to major consequences. Hence, the credibility of the payroll software is something that you should research by checking ISO certifications, other equivalent ratings, and reviews on third-party websites.

Now that you know exactly what to look for in Payroll Software. Let’s check the 10 Best Payroll Software Solutions that should be on your Shopping list.

QuikchexPagarbooksSaral PaypackRazorpayADP VistaGreytHRHRXpertKredilyHRMThreadZoho
Core Payroll Software
Attendance and Leave Tracking
Expense Tracking
Employee Portal (Web + Mobile)
Flexi benefits & custom CTC
TDS and Compliance Calculations
Full suite HRMS
Salary TDS filing services
Payroll Outsourcing service
Managed Compliance service
Dedicated Account Managers

Best Payroll Software For SMEs In India


Quikchex is an easy-to-use, yet highly configurable and affordable HRMS designed to cater to Indian Payroll needs. It has a market standing of over 40 years in the HR tech and staffing industry and is one of the fastest-growing Payroll solutions companies in India, catering to hundreds of small and mid-sized businesses.

What is unique about Quikchex, relative to other payroll software solutions in the market, is that it offers a full-suite HRMS that integrates with their payroll, as well as a complete payroll outsourcing solution, that includes PF, ESIC, Professional Tax, and Salary TDS Management.

Their payroll software module is highly scalable, with a UI simple enough to work for 20-employee startups, yet configurable enough to accommodate 5000+ employee companies as well, with advanced features like Flexi-Benefits, Loans, and Advances, etc.

Moreover, every client has a dedicated Account Manager, who provides clients with payroll advisory support related to tax, compliance, or salary structures.

Quikchex Payroll Features include:

1. Easy-to-use User-Interface
2. Integration with in-house attendance, leave, and full-suite HRMS
3. Custom payroll cycles, allowances, deductions, and CTC structures
4. Ability to process arrears, variable allowances, loans, advances, and Flexi-benefits
5. Comprehensive tax declaration and investment proof submission portal
6. User-friendly ESS Portal (Mobile + Web) to view payslips, tax calculations, and Form 16s
7. Ability to generate custom payslips, FNF statements, and Salary Reports
8. Automated TDS calculation based on Investment declaration
9. Dedicated Account Manager to provide payroll outsourcing support and tax/compliance advisory


1. Easy-to-use yet highly configurable software
2. Integration with Quikchex HRMS
3. Add on Payroll Outsourcing and Compliance Management Services
4. Dedicated account manager for round-the-clock support


1. Niche modules for L&D and R&R are not available

Suitable for:

Small, Mid, and Large Sized Companies


Image Source: Pagarbooks

As the name suggests, Pagarbooks is a tool to automate the salary process of your employees. With features like Face recognition attendance tracking, one-click multiple payments, Payslip generation, and Mobile and web-based applications for employees, it is good for small companies with basic requirements. Pagarbooks has an easy-to-use user interface but it is worth noting that it is a payroll automation tool and not a complete HRMS and Payroll Outsourcing Solution.

Pagarbooks features include:

1. Customizable CTC structures available
2. One-click multiple payments with automated payslips
3. Automated calculation of advances, bonuses, etc.
4. Easy-to-use mobile application
5. Face recognition and location-based attendance tracking (No biometric integration)
6. Cashbook on Mobile for expenses and reimbursement


1. One-click multiple payments options
2. Easy-to-use Mobile Application


1. Limited to payroll automation and salary processing
2. Does not have an HRMS, so will need to use a separate HRMS
3. Not scalable for large enterprises
4. No Payroll or Compliance Management Solution (filing and inspections will have to be done by you or another additional vendor)

Suitable for:

Small (<20 Employee) Companies


Image Source: Saral PayPack

Saral paypack in Hindi translates to ‘Simple Paypack’ and staying true to its name, they offer a basic Payroll solution with all features right from marking attendance to generating payslips with options of cloud-based and desktop-based versions as well. Features and functionality of Saral paypack remain limited to payroll, attendance, and leave tracking and may not be ideal for companies looking for a comprehensive HRMS Solution.

Features of Saral Paypack include:

1. End-to-end payroll management with custom salary structures
2. Generation of Payslips and other documents
3. Leave tracking with custom policies
4. Real-time Attendance tracking with biometric integration (Available in the premium plan)
5. PF, ESIC, PT calculations with Form 16 generation
6. ESS with reimbursement claims
7.Easy-to-use Mobile application


1. Simple user-friendly UI
2. Cloud and Desktop based options are available


1. Basic features like Real-time Attendance tracking available in add-on premium plans
2. Not ideal for companies looking for a complete HRMS Solution
3.No Payroll or Compliance Management Solution (filing and inspections will have to be done by you or another additional vendor)

Suitable for:

Small to Mid-sized firms


Image Source: RazorPay

Starting as a gateway provider and neobank provider in 2015, Razorpay has gained the trust of users in the banking industry. Recently, through the acquisition of Opfin, they entered the payroll market. Razorpay offers a complete automation solution for auto dispersion of payroll, taxes, and compliance calculations. It is built for startups with a simple requirement and modules of Razorpay are limited to payroll, compliance, and attendance tracking.

Razorpayx payroll includes:

1. Complete automation in payroll processing
2. Automated PF, ESIC, and PT compliance calculations
3. Automatic bifurcation of CTC, Allowances, HRA, etc.
4. Seamless Slack Integration
5. Basic attendance and leave tracking system
6. Letter generation system
7. Monthly and quarterly TDS calculation
8. Auto disbursement of salaries


1. Auto disbursement of payroll and compliance payments
2. Slack Integration available


1. Not ideal for 50+ employee companies due to limited configurability
2. Not ideal for companies looking for a complete HRMS solution

Suitable for:

Small-sized startups


Image Source: ADP

ADP or Automatic Data Processing is another renowned player in the HR Tech Industry, especially in the US. Their suite of products has been categorized based on employee strength and the global presence of its clients. ADP Vista is ideal for small to mid-size companies looking for a complete payroll solution while software like ADP Celergo and ADP GlobalView offer a full-fledged cloud-based HRMS for larger enterprises with a global presence. They also offer to provide a range of other services like ‘SmartComplaince’ for automated compliance tracking and Payroll Outsourcing services as well.

ADP Vista features include:

1. Automated payroll and tax calculations
2. Updates on compliance legislation
3. Auto generation of payslips
4. Easy-to-use ESS portal for employees
5. Attendance and Leave Tracking
6. Quarterly TDS Filings and reimbursement claims
7. Add on Payroll Outsourcing and Compliance filing services


1. Long standing in the industry
2. Add on Payroll Outsourcing and Compliance services


1. Niche HRMS modules not available
2. Expensive for SME Budgets

Suitable for:

Mid to Large size Enterprises


Image Source: GreytHR

GreytHR has been in the industry for more than 25 years and has built expertise in Payroll and HR Management over these years. GreytHR also enjoys credibility in the industry with thousands of customers in India. They offer a comprehensive HR solution that enables users to manage and quickly access employee data and reports.

GreytHR features include:

1. Complete automated payroll processing
2. Configuration of complex salary structures
3. Automated payroll inputs and payslips
4. Biometric, geo-fencing and face-recognition attendance tracking
5. Comprehensive Overtime and Shift Management
6. Customizable Leave tracking
7. ESS web and mobile-based portal
8. Payroll and Statutory Compliance Calculations


1. Easy to use.
2. Long standing in the industry.


1. Modules like PMS and recruitment are not available.
2. No Payroll or Compliance Management Solution (filing and inspections will have to be done by you or another additional vendor)

Suitable for:

Small to Mid-sized companies


Image Source: HRXPERT

Taking advantage of the notable name of Marg ERP in the accounting tech industry, HRXpert quickly gained traction for being dependable and expertly crafted payroll software. They also offer some basic HR functions like attendance tracking, biometric integration, the ability to generate reports, and calculated and file payroll compliances for their users. Considering all these features, it is good for small to mid-size companies for running and managing their payroll.

HRXpert features include:

1. Complete payroll automation with multi-salary structures
2. Multiple leave policies and shift management
3. Real-time Biometric Integration
4. Arrears and Increment payments
5. Payslips and FNF Settlements
6. Asset Management System


1. Payroll Outsourcing and Compliance Management services are available
2. Add on Asset Management System


1. Limited to payroll and attendance features
2. Not ideal for larger enterprises looking for an HRMS Solution
3. No Payroll or Compliance Management Solution (filing and inspections will have to be done by you or another additional vendor)

Suitable for:

Small to Mid-sized firms


Image Source: Kredily

Kredily has recently stepped into the Payroll Software Industry targeting small to medium-sized businesses.  They offer a ‘freemium’ plan to its users with limited functionality and is good for companies below 25 employees max data storage offered in this plan is 250MB. Any additional functions in this plan are chargeable. They also provide a payout gateway solution known as ‘KREDPAY’ which is a plus for companies looking for a direct payment solution for salary disbursements.

Kredily features include:

1. Freemium plan with limited functionality
2. Customizable salary structure
3. Bank integration for salary payouts
4. Bank transfers from ‘KREDPAY’
5. PF, ESCI, PT, and TDS Compliance calculations
6. Automated payslip generation
7. Real-time biometric integration
8. Expenses and leave workflow


1. Dedicated features like ‘KREDPAY’ for direct salary transfers.
2. The basic plan is affordable


1. Free plans limit user database to 250MB which is not recommended for even small companies
2. Lack of Complete HRMS option
3. Basic features are offered as chargeable add-ons
4. No Payroll or Compliance Management Solution (filing and inspections will have to be done by you or another additional vendor)

Suitable for:

Small to Mid-sized companies


Source: HRM Thread

HRM Thread developed by Sensys Technologies is an HR and Payroll Software for small to mid-sized businesses looking for an affordable and easy-to-access system with Payroll Outsourcing and Compliances Management facilities. They offer a web-based as well as on-premise or desktop-based solution.

HRM Thread features include:

1. Web-based and Desktop based offerings
2. Salary structure configuration
3. End to end Payroll Outsourcing and TDS Management
4. PF, ESCI, PT, and other compliance filings
5. FNF & Investment declaration Workflows
6. HR Letters and Documents Workflow
7. Real-time biometric integration


1. Cloud-based and Desktop based solutions are available
2. Add on Payroll Outsourcing and Compliance Management services


1. Not scalable for Large Enterprises

Suitable for:

Small to Mid-size companies


Image Source: ZohoPayroll

Zoho Payroll is a global brand in the HR Industry trusted by companies around the world. They offer an end-to-end payroll and HRMS solution with integration and customization options to their users.  However, given its target market, it may not be ideal for companies looking for a local payroll software vendor and may not offer certain functions tailored toward Indian companies.

Zoho payroll features include:

1. Automated payroll, TDS, and compliance calculations
2. Premium UI Experience and user-friendly ESS portal
3. Third-party integrations available
4. Payroll approval workflows
5. Payroll and Compliance reports


1. Integration with other Zoho products like Zoho books, Zoho people, etc.
2. The market standing of Zoho


1. Zoho’s HRMS is a separate solution, which requires additional integration and costs
2. No Payroll or Compliance Management Solution (filing and inspections will have to be done by you or another additional vendor)
3. Not very configurable for more complex payroll scenarios (e.g. Flexi-benefits management)

Suitable for:

Mid to Large size companies

To summarize, there are quite a few best payroll software solutions in India today. However, when deciding on a solution, you should choose one that meets your requirements from a cost, feature, service, integration perspective, and whether they offer other payroll management services. Payroll and HRMS software go hand-in-hand with each other so we would also recommend you check our recent article on the Best HRMS software for SMEs in India before taking your final call.

If you haven’t made up your mind yet you can contact our experts at 0221248830 and have a detailed discussion on what’s best for you