Expert verified With multiple options available and new ones coming, finding the best ecommerce accounting software in India can get overwhelming.
Explore with us some of the best ecommerce softwares in India – free, budget-friendly and enterprise level, catering to all your ecommerce accounting needs.
Why Ecommerce Businesses in India Need Specialized Accounting Software
Ecommerce businesses in India operate in a highly regulated, fast-moving environment that traditional tools struggle to manage.
Limitations of Traditional Accounting Software for E-commerce in India
| Limitation | Core Issue | Impact |
| Manual Data Entry | Built for single invoice entries, not hundreds of daily e-commerce transactions. |
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| Lack of E-commerce Reporting | Only standard P&L/Balance Sheet, no e-commerce insights. |
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| Poor Integrations | Limited or no API links with marketplaces, banks, CRM, shipping, etc. |
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| Limited Multi-Channel Support | Handles single sales stream, struggles with multiple platforms. |
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| Weak Inventory Management | Basic modules, no real-time multi-channel sync. |
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Reasons to Choose Specialized Ecommerce Accounting software
1. Simplified GST and TCS Compliance
India’s GST system is complex, especially with TCS deductions by marketplaces like Amazon and Flipkart.
Ecommerce accounting software automates GST invoicing, applies correct tax rates, handles TCS reconciliation, and generates e-invoices and e-way bills, minimizing errors and ensuring compliance.
2. Multi-Channel Sales Integration
Selling across platforms like Amazon, Flipkart, Shopify, and more, creates fragmented data.
Specialized ecommerce accounting software integrates all platforms, consolidating sales, fees, and taxes into one dashboard, eliminating manual downloads and reconciliation delays.
3. Automated Transaction Reconciliation
Ecommerce involves multiple fees and payment components.
Accounting tools fetch data via APIs (e.g., Razorpay, Paytm) and auto-match transactions with invoices and bank deposits, ensuring accuracy and identifying discrepancies early.
4. Real-Time Inventory and Order Management
Manual inventory tracking leads to overselling or stockouts.
Ecommerce accounting and bookkeeping tools sync inventory across platforms in real-time, helping manage stock, returns, and working capital efficiently.
5. Handling Returns, Refunds, and Adjustments
Returns impact revenue, stock, and tax records.
Accounting software for ecommerce helps adjust inventory, reverse entries, recalculate taxes, and claim eligible GST refunds, ensuring accurate books and profitability.
6. Accurate Profitability Tracking
Gross sales hide true costs like commissions, fees, and discounts.
Ecommerce software breaks down every order to show real net profit by product, category, or channel, enabling smarter business decisions.
7. Real-Time Financial Reporting and Business Intelligence
Traditional accounting tools offer delayed insights.
Modern platforms provide real-time dashboards on sales, GST, cash flow, inventory, and top products, empowering data-driven decisions.
8. Scalability and Cost Efficiency
As volume grows, manual processes become unsustainable.
Cloud-based tools scale effortlessly, automate tasks, and reduce the need for additional staff, boosting efficiency and accuracy.
9. Enhanced Compliance and Fraud Detection
High transaction volumes risk unnoticed errors or fraud.
Ecommerce tools offer built-in checks, anomaly alerts, and audit-ready reports, protecting against legal and financial risks.
Top Features to Look for in the Best Ecommerce Accounting Software in India
We have categorised the features into essential or non-negotiable, advance or good to have features and Indian compliance specific features:
Essential Features
1. Multi-Channel Integration: Most Indian sellers operate across platforms Amazon, Flipkart, Shopify, WooCommerce, etc.
- Native integrations with major platforms
- Auto-sync for orders, payments, returns, fees, and discounts
- Support for custom sites via plugins or APIs
Ensure it pulls full financial data, including returns, shipping charges, discounts, and promotions.
2. Automated Data Synchronization: Thousands of monthly transactions make manual syncing inefficient.
- Real-time or scheduled sync for orders, refunds, and fees
- Auto-tagging to correct income/expense categories
- Settlement file support (Razorpay, PayU, Amazon Pay, etc.)
3. GST Compliance & Invoice Automation: GST is mandatory and complex, using ecommerce software reduces risk.
- Auto GST calculation (CGST/SGST/IGST) per invoice
- Auto-populated GSTR-1, GSTR-3B, and GSTR-9
- E-invoicing and E-way bill generation
- Audit trail for compliance checks
4. Inventory & COGS Tracking: Inventory errors hurt revenue and trust. Accurate COGS is vital for true profit visibility.
- Real-time stock updates across channels
- Multi-warehouse support
- SKU-wise or batch-wise COGS tracking
- Auto-adjustments after sales, returns, or transfers
- Alerts for low/aging inventory
5. Payment Gateway & Bank Reconciliation: Payouts differ from invoice amounts due to fees, TDS, and refunds.
- Automated reconciliation of payouts with orders
- Breakdowns for fees, TDS, GST
- Multi-bank account support
6. Financial Reporting & Analytics: Data-driven decisions need clear reports.
- P&L, balance sheet, and cash flow statements
- Platform/product/time-wise reports
- Custom dashboards with real-time KPIs
- Export options (Excel, PDF, API)
- Role-based access control for team members
Advanced Growth Features
1. Profitability Analysis (SKU/Platform-wise): Track true profitability beyond just sales.
- Fees, commissions, and logistics deducted profit per channel
- Product-level profit and return analytics
- Region/campaign ROI tracking
2. Multi-Currency Support: For global sales via Amazon Global, Shopify, etc.
- Auto FX conversion (USD, EUR, GBP to INR)
- FEMA-compliant cross-border reports
- Gain/loss tracking from exchange rates
3. Automated GST-Compliant Invoices: Thousands of monthly orders makes automation essential
- Customizable GST invoice templates
- Auto-invoicing with HSN, taxes, and buyer info
- Bulk invoice generation & dispatch (SMS/email)
- QR code & IRN generation for B2B e-invoicing
4. Expense Categorization & and Tracking: Track and tag digital expenses accurately.
- Bank/credit card auto-imports
- Rule-based categorization (e.g., “Google Ads” → Marketing)
- GST input credit (ITC) treatment
- Visual dashboards for trends
5. Logistics & Shipping Integration: Shipping is costly, tracking every rupee.
- Integration with Shiprocket, Delhivery, Blue Dart, etc.
- Sync AWB, delivery status, and charges
- Customer tracking portals
- Auto-accounting of logistics fees
6. API connectivity: Allows automated syncing of orders, payments, refunds, and inventory
- Custom integrations with custom ecommerce platforms or tools
- Real-time data sync & webhooks
7. Mobile App Access
Ecommerce runs 24/7, you need access anytime.
- iOS and Android apps
- Quick access to reports, invoices, and alerts
- Biometric login & real-time push notifications
India-Specific Must-Haves
1. GST Return Filing (GSTR-1, GSTR-3B, GSTR-9):
- Map each transaction to correct GST slabs
- Auto-populate returns
- Reconcile GSTR data with GSTN (GSTR-2A/2B)
- Handle TCS (Tax Collected at Source) reconciliation
2. TDS Calculation and Reporting: For vendor and advertising payments subject to TDS:
- Auto-calculates TDS as per Section 194Q and others
- Maintains deduction ledgers
- Generates reports and pre-filled return files
3. HSN/SAC Code Management: GST compliance requires mapping each product/service to:
- Correct HSN codes (goods) or SAC codes (services)
- Auto-fill HSN in invoices and returns
4. State-Wise GST Calculations: Handles intra-state vs inter-state tax logic:
- CGST + SGST for local sales
- IGST for inter-state sales
- Automatically applied based on buyer’s location
5. Support for Indian Payment Gateways: Integrates with major gateways like Razorpay. PayU, CCAvenue, PhonePe for Business, etc.
This ensures accurate tracking of fees, GST, and net payouts.
6. Regional Language Support: For diverse teams across India, some tools offer UIs and reports in Hindi, Tamil, Marathi, Telugu, etc.
8 Best Ecommerce Accounting Software in India: Top Picks
Here are some of our most recommended ecommerce specific accounting softwares:
Zoho Books
This cloud-based accounting software is tailored for Indian businesses and offers seamless integration with ecommerce platforms, powerful automation.
Top Features:
- GST-compliant invoicing, filing, and audit trail
- Automated bank feeds and expense tracking
- Inventory and sales order management
- Mobile apps and client portal access
Ecommerce Strengths:
- Native integrations with Shopify, Amazon, Flipkart, WooCommerce
- Payment gateway reconciliation (Razorpay, Paytm, etc.)
- Automated order tracking and multi-channel sales sync
Limitations:
- Ecommerce features like marketplace sync available only in higher-tier plans
- Slight learning curve for non-technical users
Best For: Online-first ecommerce startups and SMBs needing a scalable, cloud-native solution with rich automation and integrations.
Tally Prime
Known for its unmatched GST compliance and deep financial capabilities, Tally Prime is used by accountants across India. It’s ideal for businesses with both offline and online operations.
Top Features:
- Comprehensive GST support (GSTR-1, GSTR-3B, GSTR-9 filing, e-invoicing)
- Advanced inventory management (batch-wise, godown-wise)
- Financial reporting (P&L, Balance Sheet, Trial Balance)
- Multi-currency and bank reconciliation
- Secure remote access via Tally.NET
Ecommerce Strengths:
- Customizable via third-party integrations to connect with platforms like Amazon and Flipkart
- Ideal for businesses needing detailed inventory and tax handling across multiple channels
Limitations:
- Not cloud-native; primarily desktop-first
- Requires manual effort or API integrations for ecommerce data sync
- UI feels dated compared to cloud solutions
Best For: Established ecommerce businesses with low-to-moderate online order volumes and strong offline sales presence.
Vyapar
Vyapar is a simple, mobile-first accounting app designed for small Indian businesses. It’s perfect for GST billing, inventory, and basic reporting.
Top Features:
- GST-compliant invoicing and tax calculation
- Inventory tracking with barcode scanning
- Offline mode and real-time data backup
- P&L, cash flow, and basic analytics
Ecommerce Strengths:
- Quick invoice generation for online orders
- Low-cost and beginner-friendly mobile access
Limitations:
- No direct marketplace integrations; manual data entry required
- Limited reporting and automation for growing ecommerce needs
Best For: Micro-businesses and new ecommerce sellers looking for a low-cost, mobile-accessible tool for basic accounting.
Sage 50cloud
A hybrid desktop-cloud accounting software offering advanced financial tools and cloud-enabled collaboration for growing businesses.
Top Features:
- Multi-currency accounting and robust reporting
- Inventory, job costing, and role-based access
- Microsoft 365 integration and remote access
Ecommerce Strengths:
- Suitable for custom integrations with ecommerce platforms
- Scalable for growing ecommerce operations with complex needs
Limitations:
- Not built specifically for Indian marketplaces
- Requires third-party connectors for ecommerce sync
- Higher pricing and steeper learning curve
Best For: Medium to large businesses seeking a balance between desktop stability and cloud collaboration, with custom ecommerce integration capabilities.
Marg ERP 9+
It is a comprehensive Indian ERP designed for distribution, retail, and pharma businesses. It features in-depth inventory, billing, and GST management.
Top Features:
- GST filing, e-invoicing, e-way bills
- Barcode-based inventory and batch management
- Vendor management and stock reorder tracking
- Mobile app support
Ecommerce Strengths:
- Handles high-volume inventory well
- Useful for sellers with both online and offline distribution models
Limitations:
- No native ecommerce integrations; relies on manual imports or external tools
- Dated UI and longer onboarding time
Best For: Wholesale and high-inventory ecommerce businesses with distribution roots, needing strong control over stock and taxation.
AlignBooks
This is again a cloud-based Indian accounting platform offering GST compliance, automation, and ecommerce-oriented features.
Top Features:
- GST-ready invoicing and bank reconciliation
- Multi-user collaboration and role-based access
- Payroll management and mobile support
Ecommerce Strengths:
- Integrates with ecommerce platforms and payment gateways
- Automated invoice generation and order sync
Limitations:
- Smaller ecosystem of third-party tools than Zoho or Tally
- May require configuration for advanced ecommerce use cases
Best For: Growing ecommerce startups and MSMEs transitioning to cloud software from traditional desktop tools.
Gofrugal
Gofrugal is an ERP solution focused on retail, food, and distribution, with strong omnichannel capabilities and POS integration.
Top Features:
- POS, inventory, and order management
- Mobile apps for field staff and delivery
- Cloud-enabled with offline backup
Ecommerce Strengths:
- Syncs inventory across online and physical stores
- Great for businesses running physical + digital channels
Limitations:
- Overkill for pure online sellers
- Limited ecommerce automation out of the box; needs configuration
Best For: Retailers with both physical stores and online presence looking for an integrated ERP + POS + ecommerce system.
SAP Business One
It is an enterprise-grade ERP offering complete business process automation, advanced reporting, and scalability for large ecommerce operations.
Top Features:
- Finance, CRM, sales, and supply chain management
- Multi-location, multi-currency, and compliance support
- Custom APIs and analytics dashboards
Ecommerce Strengths:
- Handles large order volumes across channels
- Offers centralized visibility across sales, inventory, and operations
Limitations:
- Expensive and complex to implement
- Requires IT support and long setup timelines
- Ecommerce integrations depend on third-party connectors
Best For: Large-scale ecommerce companies or omnichannel enterprises requiring full ERP capabilities with international scalability.
Choosing the Right Accounting Software for Your Ecommerce Business
Let’s take a look at some of the best accounting softwares for ecommerce based on their size and industry –
Business Size Considerations:
| Category | Key Considerations | Recommended Solutions & Features |
| Startups (0–100 orders/month) |
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| Growing Businesses (100–1000 orders/month) |
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| Large Enterprises (1000+ orders/month) |
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Industry-Specific Recommendations:
| Category | Key Considerations | Recommended Solutions & Features |
| Fashion & Apparel | Inventory with variants (size, color, style) |
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| Electronics | Warranty & serial number tracking |
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| Food & Beverages | Batch & expiry tracking, FSSAI compliance |
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| Healthcare | Batch tracking & Regulatory compliance |
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| Books & Media | ISBN management & Royalty calculations |
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Roadmap & Best Practices to Implement E-Commerce Accounting Softwares
Implementing accounting software for ecommerce has to be done right to get all its benefits. Here’s an overview of some best practices:
Phase 1: Pre-Go-Live Checklist
1. System Configuration
- GST & Tax Setup: Configure CGST, SGST, IGST, HSN/SAC codes, and TCS rules.
- Integrations: Connect platforms (Amazon, Flipkart, Shopify) and gateways (Razorpay, PayU).
- Chart of Accounts: Customize for ecommerce—COGS, returns, logistics, ad spend.
- User Roles: Set role-based permissions (Admin, Finance, Ops).
2. Data Validation & Migration
- Clean Data: Standardize SKUs, remove duplicates.
- Trial Migration: Test with sample data; reconcile with existing systems (Tally, Excel, etc.).
- Opening Balances: Reconcile bank, inventory, GST credits, receivables/payables.
- Product Sync: Ensure SKU-level stock matches across platforms.
3. User Training
- Role-Specific Training: Train teams on invoices, reports, and reconciliations.
- Documentation: Provide guides, videos, cheat sheets.
- Sandbox Testing: Practice in a test environment before go-live.
4. Backup & Cutover Planning
- Legacy Backup: Save current system data before switching.
- System Backup: Enable daily/weekly auto-backups.
- Cutoff Date: Plan go-live around period-end.
- Parallel Run (Optional): Run both systems briefly to compare results.
Phase 2: Post-Implementation Optimization
1. Monitor Performance
- KPIs: Track reconciliation accuracy, time-to-close books, GST errors.
- System Logs: Monitor sync failures, order mismatches, and uptime.
2. Collect Feedback
- Channels: Use Google Forms, Slack, or team check-ins.
- Review Loop: Hold sessions 2–4 weeks post-launch to resolve issues.
3. Refine Processes
- Automation: Eliminate manual steps (e.g., recurring invoices).
- GST Workflow: Automate exports and reconciliation.
- Update SOPs: Reflect new workflows in internal documentation.
4. Adopt Advanced Features
- Roll out advanced tools like multi-currency, AI categorization, dashboards.
- Introduce features gradually to avoid overwhelm.
5. Support & Maintenance
- Internal Champions: Identify power users to support peers.
- Vendor Support: Share contacts and escalation paths.
- Quarterly Reviews: Evaluate system use and request updates.
6. Data Security & Audits
- Audit Trails: Ensure all changes are logged.
- Access Review: Revoke old logins and manage roles.
- Cybersecurity: Use 2FA, encryption, and comply with India’s DPDP Act.
Why Choose PKC for Ecommerce Accounting Software Selection & Implementation
✅ Seamless integration with major sales channels
✅ Real-time synchronization of all transactions
✅ Customized reporting for ecommerce metrics
✅ Manages complex multi-channel inventory efficiently
✅ Provides dedicated ecommerce accounting specialists
✅ Streamlines reconciliation from various payment gateways
✅ Ensures accurate financial data consolidation
✅ Simplifies complex ecommerce accounting workflows
✅ Provides end-to-end implementation support
Learn more about our accounting services here
FAQs on Ecommerce Accounting Software
Ecommerce accounting software is a tool designed to manage online sales, GST, invoices, and inventory.It integrates with platforms like Amazon, Flipkart, and Shopify to make bookkeeping easier.
Because GST compliance, multi-channel sales, and online payments make accounting complex.Specialized software saves time, reduces errors, and ensures compliance with Indian tax laws.
Popular choices include Zoho Books, TallyPrime, Vyapar, Busy, and Marg ERP. The best one depends on your business size, budget, and selling platforms.
Some apps like Vyapar and Zoho Books (free plan for small businesses) offer limited free features. But for scaling ecommerce businesses, a paid plan is usually necessary.
Yes, many accounting tools support direct integrations with Amazon, Flipkart, and other marketplaces. This ensures all sales data flows into one system without manual uploads.
