Top 10 Accounting Software for Ecommerce Businesses in India (2025)

Running an Ecommerce business in India in 2025 is no longer just about listing products and processing payments.

With increasing multi-channel sales, complex GST compliance, TDS/TCS regulations, and real-time inventory tracking, choosing the right accounting software for Ecommerce has become a critical success factor.

A powerful accounting solution can automate financial operations, reduce errors, reconcile payouts, and provide actionable insights, allowing founders to focus on growth, not spreadsheets.

In this guide, we explore the Top 10 Accounting Software for Ecommerce Businesses in India. Each of these solutions is India-compliant and capable of supporting Ecommerce workflows for platforms like Amazon, Flipkart, Shopify, WooCommerce, and other D2C channels.

Why Ecommerce Businesses Need Robust Accounting Software

✅ Automated bookkeeping & reconciliation: eliminate manual data entry.

📊 Real-time insights & dashboards: track profitability, cash flow, and margins.

🧾 GST-ready and tax-compliant: meet Indian regulatory standards effortlessly.

🛍️ Ecommerce channel integrations: sync orders, inventory, returns, and payouts.

🧠 Scalable solutions: adapt to growing transaction volumes and multiple channels.

Key Features to Look for in Ecommerce Accounting Tools

When choosing the right accounting solution, look for:

• Automation capabilities – auto-sync of transactions, invoices, and ledgers.
• Marketplace & platform integrations – Shopify, Amazon, Flipkart, WooCommerce, & other important platforms for your business.
• Tax compliance & GST filing support – auto-calculations and reports.
• Inventory and order management – real-time stock visibility.
• Multi-user access & security – scalable for growing teams.
• AI-powered insights – accurate financial forecasting and analytics.

Top 10 Accounting Software for Ecommerce in India (2025)

1. Suvit – Best for Ecommerce Accounting Automation

Website: Suvit.io

Suvit is designed to automate Ecommerce accounting for Indian businesses.

• Key Features:

  • Auto-import of data from different marketplaces excels
  • Tally integration for seamless ledger management
  • Real-time reports and automated reconciliations
  • GST automation

• Best For: Ecommerce brands, sellers, and D2C businesses looking to reduce manual accounting workload.

• Why It Stands Out: Suvit minimizes manual work, ensuring accurate financial records and timely compliance.

2. TallyPrime – Most Popular Accounting Software in India

• Key Features:

  • GST-ready accounting and invoicing
  • Inventory and stock management
  • TCS, TDS, e-invoicing compliance

• Best For: MSMEs, online retailers, and hybrid ecommerce models.

• Highlight: Widely used in India with third-party connectors available for Ecommerce platforms.

3. Zoho Books – Cloud-Based Accounting for Modern Sellers

• Key Features:

  • GST-compliant invoicing and filing
  • Integration with Zoho Commerce and other platforms
  • Real-time financial insights and mobile access

• Best For: Growing Ecommerce businesses looking for a flexible, cloud-based accounting tool.

• Highlight: Built in India, trusted globally.

4. NetSuite (India Localization) – Enterprise-Grade ERP for Ecommerce

• Key Features:

  • Full ERP with accounting, order, and inventory modules
  • Localization for GST, TDS, and Indian compliance
  • Advanced reporting and automation

• Best For: Large Ecommerce enterprises and high-volume sellers.

• Highlight: Scalable for complex multi-channel operations.

5. ERPNext – Open Source ERP for Custom Ecommerce Workflows

Website:

• Key Features:

  • Built-in ecommerce, accounting, inventory, and website modules
  • GST compliance and localized features
  • Fully customizable open-source platform

• Best For: Tech-savvy Ecommerce brands seeking flexibility.

• Highlight: Developed in India, ideal for D2C and multi-channel operations.

6. Marg ERP – Ideal for Inventory-Heavy Ecommerce Sellers

• Key Features:

  • Ecommerce seller modules with order sync
  • GST-ready invoicing and stock tracking
  • Multi-branch management

• Best For: FMCG, retail, and multi-location Ecommerce businesses.

• Highlight: Trusted by Indian businesses with solid inventory features.

7. BUSY Accounting Software – Simplified Accounting for SMEs

• Key Features:

  • Inventory and billing management
  • GST and TDS support
  • Integration support for Ecommerce setups

• Best For: Small to mid-sized Ecommerce sellers.

• Highlight: Easy to implement, affordable, and reliable.

8. RealBooks – Built for Ecommerce Accounting

• Key Features:

  • Multi-channel Ecommerce accounting
  • Payout reconciliation for Amazon, Flipkart, Shopify
  • GST reporting and tax filing

• Best For: D2C brands, multi-channel Ecommerce sellers.

• Highlight: Tailored for Ecommerce operations in India.

9. TEZ ERP – Unified ERP for Indian Businesses

• Key Features:

  • Centralized accounting and inventory
  • Indian compliance support
  • Multi-location data sync

• Best For: Retail and B2C Ecommerce brands.

• Highlight: Homegrown ERP with growing Ecommerce support.

10. GNUKhata – Open Source Accounting Software for Budget-Conscious Sellers

• Key Features:

  • Core accounting and inventory
  • Customizable workflows
  • GST-ready basic features

• Best For: Early-stage Ecommerce businesses and startups.

• Highlight: Free and open-source, great for building custom solutions.

Comparison Table: Best Accounting Software for Ecommerce in India (2025)

No.	Software Name	Country of Origin	Ecommerce Integration	GST & Tax Compliance	Automation Level	Ideal Business Size	Pricing Model	Key Strength
1	Suvit	India	✅ Strong (Amazon, Shopify, Flipkart)	✅ Fully GST-ready	⭐⭐⭐⭐ High	Small to Enterprise	Subscription-based	Automation-first, Tally integration
2	TallyPrime	India	✅ via connectors	✅ Full	⭐⭐ Moderate	MSMEs, Retailers	Perpetual + Subscription	Widely used, strong compliance
3	Zoho Books	India	✅ Native & API	✅ Full	⭐⭐⭐ High	Small to Mid-size	Subscription-based	Cloud-based, easy integrations
4	NetSuite	USA (localized)	✅ Native	✅ With localization	⭐⭐⭐⭐ High	Mid to Enterprise	Premium Subscription	Full ERP suite, advanced capabilities
5	ERPNext	India	✅ Native ecommerce & API	✅ Localized support	⭐⭐⭐⭐ High	Small to Large	Open-source + Paid	Highly customizable, open-source
6	Marg ERP	India	✅ Ecommerce seller module	✅ GST-ready	⭐⭐ Moderate	MSMEs, Retailers	License + Subscription	Good inventory management
7	BUSY Accounting	India	✅ Basic integration	✅ Full	⭐⭐ Moderate	Small to Mid-size	License + Subscription	Easy to use, cost-effective
8	RealBooks	India	✅ Strong	✅ Full	⭐⭐⭐ High	Small to Mid-size	Subscription-based	Ecommerce-focused, payout reconciliation
9	TEZ ERP	India	✅ Moderate	✅ Full	⭐⭐ Moderate	Retail & SMEs	Subscription-based	Local ERP, growing marketplace support
10	GNUKhata	India	⚠️ Custom integration	✅ Basic	⭐ Low	Startups, NGOs	Free (Open-source)	Cost-effective, customizable

How to Choose the Right Accounting Software for Your Ecommerce Business

Before making your decision, assess your specific needs:

🏪 Business size and complexity – Solo seller or multi-channel enterprise?

🔗 Marketplace integrations – Shopify, Flipkart, Amazon, WooCommerce.

🧾 GST and compliance requirements – Ensure proper e-invoicing and tax filing.

🚀 Automation level – Reduce manual tasks to scale efficiently.

💸 Budget and support – Balance between cost, scalability, and local support.

Future-Proof Your Ecommerce Finances

The Ecommerce industry in India is expanding rapidly, and so are financial complexities. By investing in the right accounting software, businesses can simplify GST compliance, automate reconciliation, improve cash flow visibility, and scale sustainably.

Suvit leads the list for its automation-first approach, followed by trusted names like Tally, Zoho Books, and RealBooks, ensuring that Ecommerce sellers have access to powerful, localized solutions.

👉 Whether you’re a small D2C brand or an enterprise seller, choosing the right tool today can save you countless hours, and empower smarter decisions tomorrow.

FAQs

1. Which is the best accounting software for Ecommerce in India?

Suvit, TallyPrime, Zoho Books, RealBooks, and NetSuite are among the best accounting software for Ecommerce in India, offering GST compliance, automation, and marketplace integrations.

2. What features should Ecommerce businesses look for in accounting software?

Key features include automation, inventory and order management, tax compliance, marketplace integrations, and real-time reporting.

3. Are there free or open-source accounting software options for Ecommerce in India?

Yes. ERPNext and GNUKhata are open-source solutions that can be customized for Ecommerce businesses, especially startups and small sellers.