E-commerce sellers in India face a different GST compliance burden from ordinary traders. A seller dealing through Amazon, Flipkart, Meesho, Myntra, Shopify or its own D2C website must track marketplace-wise sales, returns, cancellations, TCS, GST invoices, B2B/B2C classification, HSN-wise reporting, GSTR-1, GSTR-3B, 2A/2B reconciliation, e-invoicing, e-way bills and payment settlements.
A good GST software for e-commerce sellers should therefore do more than generate invoices; it should reduce manual reconciliation and help match marketplace reports with GST returns.
Below are 10 GST/accounting/e-commerce management software options suitable for Indian e-commerce sellers.
| No. | Software | Best For | Key Features | Pricing |
| 1 | ClearTax GST / ClearGST | Sellers and CAs handling GST filing and reconciliation | GSTR-1 to GSTR-9C filing, reconciliation, AI matching, ERP data import, e-commerce report upload | Public plan pricing varies; third-party listings mention around ₹40,000, but confirm with ClearTax |
| 2 | Zoho Books | D2C brands and sellers needing cloud accounting | GST invoicing, accounting, inventory, reports, user access, cloud collaboration | Free plan available; paid plans with add-on users at ₹180/month or ₹150/month annually |
| 3 | TallyPrime | Sellers using accountants and offline/desktop workflows | GST filing, e-way bill, inventory, accounting, e-commerce operator-wise sales reporting | Monthly subscription ₹750/month + GST; perpetual licence commonly listed at ₹22,500 + GST single-user and ₹67,500 + GST multi-user |
| 4 | Vyapar | Small sellers needing simple GST billing | GST invoices, inventory, payments, expenses, business reports | Public pricing shown around $8.33/month to $11.67/month on Vyapar pricing page; Indian third-party reports mention paid plans from ₹1,799/year |
| 5 | BUSY Accounting Software | GST-registered sellers needing strong accounting and inventory | GST e-returns, direct GSTR-1/IFF upload, auto e-invoice/e-way bill, 2A/2B reconciliation, inventory | Basic ₹9,999, Standard ₹14,999, Enterprise ₹19,999, exclusive of GST; Standard includes GST/e-invoice/e-way bill features |
| 6 | Marg ERP | Retail/e-commerce sellers with inventory-heavy operations | GST billing, return filing, e-way bills, inventory, distribution and ERP modules | Price list shows Nano, Basic, Silver and Gold plans; examples include Nano ₹2,400 ARC and GST billing page listing Nano ₹5,550, Basic ₹10,300, Silver ₹13,900, Gold ₹26,000 depending on plan/version |
| 7 | myGSTcafe | CAs/tax professionals filing GST for multiple sellers | GSTR-1, GSTR-3B, 2A/2B reconciliation, Excel upload, unlimited GSTIN filing in some plans | Third-party listing shows Basic at ₹7,500/year and renewal at ₹3,500 + GST |
| 8 | eVanik OneWorld / Accounting Integration | Multi-channel sellers on Amazon, Flipkart, Meesho, Myntra etc. | Marketplace integrations, payment reconciliation, accounting integration, GST-compliant accounting export, order-volume-based plans | Blue starts ₹10,000 quarterly / ₹20,000 annually up to 500 monthly orders; higher plans go up to ₹3,50,000 annually before Enterprise custom pricing, excluding GST |
| 9 | GST Tool | E-commerce sellers and CAs converting marketplace data into GST reports | GSTR-1 JSON/Excel generation, online seller GST reporting, 2A/2B verification, eCom-to-Tally import | GST online tool page shows ₹149/month with 30-day free activation/trial claim |
| 10 | Unicommerce / Uniware | Larger brands and marketplace sellers needing OMS + GST-ready operations | Order management, inventory, warehouse, returns, payment reconciliation, ERP/accounting integration, Tally/TallyPrime auto-sync | Custom/demo-based pricing; plans include Standard, Professional and Enterprise, with features depending on facilities, SKUs, integrations and order volume |
For small single-channel sellers, Vyapar, GST Tool or Zoho Books may be enough because the main requirement is GST invoice creation, basic sales tracking and simple return preparation. For sellers already working with accountants, TallyPrime, BUSY or Marg ERP are more practical because accountants in India are comfortable with their workflows and they offer strong accounting, inventory and GST reporting.
For high-volume e-commerce sellers, the bigger problem is not only GST filing but reconciliation. Marketplace settlement reports often include commission, shipping fees, penalties, returns, cancellations, TCS and payment adjustments. For this category, eVanik, Unicommerce and EasyEcom-type platforms become more relevant because they connect marketplace operations with accounting and reconciliation. eVanik specifically publishes order-volume-based accounting integration plans and supports GST-compliant accounting integration with Tally and other ERPs.
ClearTax GST is useful where return filing, reconciliation and GST compliance are the main pain points. It supports GST return preparation and filing from GSTR-1 to GSTR-9C, reconciliation and data import from ERP or custom mappers.
Best overall choice: For a growing e-commerce seller, the safest combination is often eVanik/Unicommerce for marketplace operations + TallyPrime/BUSY/Zoho Books for accounting + ClearTax/GST Tool for return filing support, depending on volume and budget. For a very small seller, Vyapar or Zoho Books may be sufficient. For a high-volume seller selling on multiple marketplaces, choose eVanik or Unicommerce because marketplace reconciliation is usually more important than ordinary billing.
Read More: GST On Professional Fees
