Best Accounting Software for MSMEs in India
Choosing the best accounting software for MSMEs in India is no longer a luxury—it is a necessity. With increasing financial complexity, GST compliance requirements, and the need for real-time financial visibility, micro, small, and medium enterprises (MSMEs) must rely on digital tools to survive and thrive. India’s booming digital economy has given rise to several affordable and easy-to-use accounting software solutions tailored to MSMEs. These tools help streamline invoicing, expense tracking, bank reconciliations, tax filings, and more—all of which are vital to managing a business efficiently.
In this blog, we will explore why MSMEs need specialized accounting tools, the essential features to look for, and a comprehensive review of the best accounting software for MSMEs in India in 2025. Whether you are running a manufacturing unit, retail store, or service-based firm, this guide will help you make an informed decision.
Why Accounting Software is Crucial for MSMEs
Manual accounting methods are time-consuming, error-prone, and inefficient. In contrast, accounting software provides:
- Automated data entry
- Accurate financial reporting
- Compliance with GST and tax laws
- Faster invoicing and payments
- Improved decision-making
By adopting the best accounting software for MSMEs in India, businesses can eliminate repetitive tasks, avoid compliance penalties, and focus on growth.
Key Features to Look for in Accounting Software for MSMEs
Before diving into product recommendations, it’s important to understand the must-have features:
- GST Compliance: The software should support GST-compliant invoicing, e-way bill generation, and auto-calculation of tax liabilities.
- User-Friendly Interface: MSME owners often lack accounting expertise; the software must be simple and intuitive.
- Mobile Access: Given India’s mobile-first market, the software should have a robust mobile app.
- Expense Management: Ability to track spending, categorize expenses, and generate reports.
- Bank Integration: Sync with bank accounts to track deposits, withdrawals, and reconciliations.
- Multi-User Access: Different roles and permissions for accountants, staff, and business owners.
- Affordability: Cost-effective pricing plans suitable for startups and small enterprises.
Top 7 Best Accounting Software for MSMEs in India
Let us look at the top contenders for the best accounting software for MSMEs in India, based on features, user experience, pricing, and GST compatibility.
1. MyKhataExpert
MyKhataExpert is designed specifically for Indian MSMEs. It simplifies bookkeeping, GST filing, invoicing, and expense tracking in one platform.
Key Features –
- GST-compliant invoicing
- Expense and purchase tracking
- E-way bill, debit/credit note generation
- Seamless bank account integration
- Real-time reports and dashboards
MyKhataExpert is arguably the best accounting software for MSMEs in India for those looking for a single solution for invoicing, compliance, and financial management.
Pricing: Starting at less than ₹100 per month. Affordable monthly and annual plans. Custom quotes are available for enterprises.
2. TallyPrime
Tally has been a household name in Indian accounting for decades. TallyPrime brings a modern interface to its trusted functionality.
Key Features –
- Robust inventory and payroll management
- GST compliance
- Multi-currency and multilingual support
Its offline capability makes it popular among traditional businesses with limited internet access.
Pricing: INR 18,000/year (Single user license)
3. Zoho Books
Zoho Books is a cloud-based accounting software ideal for tech-savvy MSMEs.
Key Features –
- Automated bank feeds and reconciliation
- Project management integration
- Vendor portal and timesheets
- Real-time reporting dashboards
Highly scalable and integrates with other Zoho products like CRM and Inventory.
Pricing: Starts at INR 899/month
4. QuickBooks (India)
Although QuickBooks India has scaled down, global versions are still used by many Indian MSMEs via third-party vendors.
Key Features –
- Easy invoice generation
- Bank reconciliations
- Automatic tax calculations
Intuitive UI and international standards make it suitable for export-focused MSMEs.
Pricing: INR 5000–7000/year (via vendors)
5. Vyapar
Vyapar is a mobile-first accounting tool tailored for Indian small businesses.
Key Features –
- GST billing and invoicing
- Inventory and payment reminders
- Business report generation
Perfect for shopkeepers and traders who want accounting features on mobile.
Pricing: Free version available; Premium from INR 599/year
6. Busy Accounting Software
Busy caters to distributors, traders, and manufacturers with industry-specific features.
Key Features –
- Batch and expiry tracking
- GST invoicing and returns
- MIS reports and dashboards
Powerful inventory and batch tracking features are ideal for pharma, FMCG, and electronics.
Pricing: Starts at INR 9000/year
7. Marg ERP
Marg ERP is best suited for pharma and retail MSMEs that need robust inventory and billing.
Key Features –
- Barcode generation
- GST return filing
- Billing and distribution management
Industry-specific modules with powerful customization options.
Pricing: INR 7500–12000/year
How to Choose the Best Accounting Software for MSMEs in India
When evaluating the best accounting software for MSMEs in India, consider the following steps:
Step 1: Identify Your Business Needs
- Are you a service-based firm or a product-based company?
- Do you need inventory and stock features?
- Are you registered under GST?
Step 2: Evaluate Trial Versions
Most tools offer free trials. Test user experience, speed, and ease of use.
Step 3: Check for Integrations
If you use CRM, HRMS, or other tools, check whether the software can integrate seamlessly.
Step 4: Look for Support
Good customer support is essential. Live chat, phone assistance, and tutorials help with onboarding and troubleshooting.
Step 5: Compare Value, Not Just Price
The cheapest option is not always the most cost-effective. Consider time savings, features, and compliance automation.
Benefits of Using the Best Accounting Software for MSMEs in India
- Saves Time – Automates data entry, recurring invoices, and tax calculations.
- Ensures Compliance – Helps meet GST filing deadlines, avoid penalties, and maintain audit trails.
- Improves Decision-Making – Provides real-time insights into cash flow, sales, and profitability.
- Enhances Collaboration – Multi-user access allows accountants, managers, and business owners to stay on the same page.
- Scales With Business – The best accounting software for MSMEs in India can grow with your business, offering features for increasing complexity.
The Role of MyKhataExpert as a One-Stop Accounting Solution
MyKhataExpert stands out among the best accounting software for MSMEs in India for several reasons:
- All-in-One Platform: Invoicing, GST filing, expense tracking, and reporting
- User-Friendly Interface: Designed for non-accountants
- Affordable Plans: Cost-effective for startups and growing MSMEs
- Customer Support: Expert help for onboarding and compliance
Whether you are managing a retail shop or a growing manufacturing unit, MyKhataExpert simplifies your financial operations so you can focus on scaling your business.
Conclusion
The top accounting softwares for MSMEs in India empowers businesses to manage their finances with ease, ensure GST compliance, and make data-driven decisions. With several excellent options available—from MyKhataExpert and Zoho Books to Tally and Vyapar—MSMEs can find a solution that fits their unique needs and budget.
Choosing the right tool today can set your business on the path to operational efficiency and sustained growth tomorrow. Don’t wait—streamline your financial management with the power of digital accounting.
Related Frequently Asked Questions
Q. What is the best accounting software for MSMEs in India?
MyKhataExpert, TallyPrime, and Zoho Books are among the top choices for MSMEs due to their features, affordability, and GST compliance.
Q. Can I use free accounting software for my MSME?
Yes, tools like Vyapar and Zoho Books offer free versions with basic features, but paid plans offer better automation and support.
Q. Is cloud-based accounting safe for MSMEs?
Yes, reputable software providers use encryption, backups, and security protocols to ensure your data is safe and accessible only to authorized users.
Q. How does accounting software help with GST?
The best accounting software for MSMEs in India helps generate GST-compliant invoices, file returns, and avoid penalties through automation.
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