For most Indian ecommerce sellers, the best accounting software is Zoho Books or TallyPrime. Big multi-entity brands tend to land on Oracle NetSuite or SAP Business One, and small teams do fine with Vyapar or BUSY. What separates a good tool from a bad one is how it handles payment reconciliation for marketplace settlements, GST and TDS, and your inventory accounting.
Settlements are where most sellers get stuck, so here’s a quick example. An Amazon order of ₹1,000 ships on Monday. By Friday, ₹780 reaches your bank. The other ₹220 went on commission, shipping, a return adjustment, GST TCS and TDS, all folded into one payout. If your software records just the ₹780, your sales are too low, your GST return is off, and the tax credits you’re owed never get matched.
That was our main test: does the tool split each Amazon, Flipkart or Shopify payout into its parts, and how much spreadsheet work does it save at month-end? Corient is an accounting and compliance firm that works with ecommerce sellers, so we looked at everything from a bookkeeper’s side of the desk.
Quick comparison table
Use this table to shortlist the best accounting software for multi-platform e-commerce businesses before reading the full reviews.
| Software | Best for | Pricing model |
|---|---|---|
| Zoho Books | Shopify and D2C brands | Subscription |
| TallyPrime | Teams already on Tally | Licence or rental |
| Oracle NetSuite | Multi-entity enterprises | Quote-based subscription |
| SAP Business One | Manufacturer-led brands | Quote-based |
| Dynamics 365 Business Central | Microsoft-first teams | Per-user subscription |
| Odoo | One platform for store and books | Per-user subscription or open edition |
| ERPNext | Open-source control | Free if self-hosted, or paid hosting |
| BUSY | Inventory-heavy sellers | Licence-based |
| Marg ERP | High-SKU retail and FMCG | Licence-based |
| Vyapar | Small brands starting out | Low-cost subscription |
Plans and prices change often, so check each vendor’s site for current numbers.
Do you really need ecommerce-specific accounting software?
If you sell on more than one channel, probably yes. A normal ledger records a sale. Ecommerce books also need the commission, shipping deduction, return, GST TCS, TDS credit and gateway fee that come with it. Spreadsheets can cope for a few weeks. Then someone misses a refund and the month won’t close.
The Indian rules you need to track in 2026
- Income-tax Act, 2025: It replaces the 1961 Act for new tax years from 1 April 2026. Marketplace TDS, earlier under Section 194O, now sits under Section 393. The rate is 0.1% and has been since 1 October 2024, so what changed is the section number, not the rate.
- The ₹5 lakh exemption: Resident individuals and HUFs with annual sales up to ₹5 lakh through the marketplace don’t have TDS deducted, as long as they’ve given PAN or Aadhaar. It isn’t a blanket rule for every seller.
- GST TCS: Under Section 52 of the CGST Act, marketplaces collect tax at source, currently 0.5% in total, and report it in GSTR-8. It’s separate from income-tax TDS, and plenty of sellers forget to reconcile it.
- Audit trail: Companies have needed accounting software with a permanent edit log since 1 April 2023. It’s not new this year, but it’s a common reason companies stop using plain spreadsheets.
Rules and rates change, so check current figures with your CA before you file. At that point many sellers hire an ecommerce accountant or move to one of the specialist ecommerce accounting firms rather than keep patching spreadsheets.
How We Chose the Best Accounting Software for Ecommerce
We evaluated each of the accounting software tools as accounting software to be used for e-commerce business operations and not as general ledgers, based on vendor documentation and India compliance support. Check with each vendor to verify existing integrations before purchase.
Our five criteria:
- Settlement reconciliation: Shopify Accounting and Amazon Seller Accounting both rely on payout level matching, not order levels.
- Baseline for any accounting software: An e-commerce small business with inventory tracking is inventory costing, FIFO or weighted average costing, batches, and multiple warehouses.
- Compliance to India: TDS management under the Income-tax Act, 2025 & reporting for the Indian financial year.
- Audit trail and controls: an edit log that conforms to MCA requirements and role-based approvals.
Support for multi-entity, multi-currency, and open APIs for accounting for e-commerce businesses that add channels, making the system scalable. Scalability: multi-entity, multi-currency, and open APIs for accounting for e-commerce businesses that add channels.
The 10 Best Accounting Software for Ecommerce Businesses
These are the top accounting software solutions for e-commerce businesses for large and middle-sized e-commerce sellers in India from the perspective of overall fit.
1. Zoho Books (best for Shopify and D2C brands)
Zoho Books covers GST filing, e-invoicing, bank feeds and automation rules, and it sits inside the wider Zoho family. Add Zoho Inventory and you can run books and stock from one vendor across several channels.
The catch: Matching marketplace payouts usually needs Zoho Inventory or a third-party connector, and its multi-entity consolidation is lighter than NetSuite’s. Look at the current connector list for Amazon, Flipkart and Shopify before you pay.
2. TallyPrime (best if your accountant already lives in Tally)
Most Indian accountants learned on Tally, so there’s barely any retraining. TallyPrime has voucher controls, an edit log, and GST and TDS reports that your CA will recognise straight away. For companies, that edit log also covers the audit trail rule.
The catch: It’s a desktop-first product. Marketplace settlements come in through connectors, add-ons or CSV files, which is fine for a monthly close but clumsy if you want live dashboards. Tally on Cloud helps with remote access.
3. Oracle NetSuite (best for multi-entity enterprises)
NetSuite handles several subsidiaries, currencies and consolidation in one system. If you sell across borders or run more than one legal entity, that’s the appeal. Ask your implementation partner how deep the India localisation goes, because answers differ.
The catch: It’s expensive and slow to roll out. Honestly, most sellers with one company and a few marketplaces don’t need it.
4. SAP Business One (best for brands that make their own products)
If you manufacture what you sell, Business One connects production, purchasing, stock and finance. You can see landed cost per SKU instead of estimating it in a spreadsheet.
The catch: What you pay and how long setup takes depend a lot on your implementation partner. It’s too much for a trading-only or early-stage D2C brand.
5. Microsoft Dynamics 365 Business Central (best for Microsoft-first teams)
Business Central works natively with Excel and Power BI. If your finance team already builds reports in Excel, they’ll get up to speed faster here than on most ERPs.
The catch: Marketplace connectors tend to come through partners. Before signing, ask about India localisation, e-invoicing and how it handles GST TCS.
6. Odoo (best for one platform that does everything)
Odoo sells a website builder, accounting, inventory and purchasing as separate apps, so you can start with one and add the rest later. It’s handy when you want the store and the books in the same place.
The catch: Settlement matching usually relies on third-party apps or custom work, and your experience will depend on the partner who sets it up.
7. ERPNext (best if you want open-source control)
ERPNext is open-source, built in India, and very customisable. It handles batches, serial numbers and multiple warehouses, so it suits sellers with messy inventory who have a developer to lean on.
The catch: There’s no licence fee if you host it yourself, but you’ll need technical help. Reconciling marketplace settlements usually means building a custom integration.
8. BUSY (best for inventory-heavy sellers)
BUSY is an Indian accounting and inventory package with batches, serial numbers and godowns. It works for distributors who’ve started selling online and want stock depth without a steep learning curve. Anyone used to Tally will find it familiar.
The catch: Native marketplace integration is limited, so expect to import CSV files. It’s desktop-centric and not built for multi-entity reporting.
9. Marg ERP (best for high-SKU retail and FMCG)
Marg was built for retailers and FMCG sellers with thousands of SKUs. Fast billing and tight stock control matter when you run physical stores alongside online channels.
The catch: It isn’t focused on marketplace reconciliation, and reporting is shallower than in a full ERP.
10. Vyapar (best for small brands just starting out)
Vyapar is easy to learn, tracks inventory, and issues GST invoices quickly, even from your phone. For a new seller with one or two channels, it covers the basics at a low cost.
The catch: Settlement reconciliation, multi-entity support and advanced inventory are limited. Sellers on several marketplaces tend to outgrow it quickly.
Not sure which one fits? Send Corient a month of your settlement files and we’ll show you where your current books are going wrong.
Which Ecommerce Accounting Software Should You Choose?
The best accounting software for multi-platform e-commerce businesses differs from single-channel picks, so match your accounting software for the e-commerce business shortlist to size, channels, and stock complexity:
| Your situation | Try | Why |
|---|---|---|
| Multiple entities and currencies | Oracle NetSuite | Consolidation in one system |
| Manufacturer selling online | SAP Business One | Production linked to finance |
| Team already trained on Tally | TallyPrime | Lowest retraining cost |
| Microsoft-first reporting | Dynamics 365 Business Central | Excel and Power BI |
| Fast-growing Shopify store | Zoho Books | Automation and ecosystem |
| High-volume Amazon and Flipkart seller | NetSuite, or Zoho Books with a connector | Settlement matching |
| Small seller tracking stock | BUSY or ERPNext | Batch and warehouse depth |
Not sure which is the best accounting software for an e-commerce business in your category? Run a two-week pilot with last month’s settlement files and compare how many entries each tool posts automatically.
How settlement reconciliation works, with numbers
Back to that ₹1,000 Amazon order. A good tool posts the net payout and every deduction as its own entry. The split below is only an illustration, and it ignores GST on marketplace fees to keep things readable.
| Account | Debit (₹) | Credit (₹) |
|---|---|---|
| Bank (net payout) | 780 | |
| Marketplace commission expense | 130 | |
| Shipping and fulfilment fees | 60 | |
| Sales returns and refund adjustment | 24 | |
| GST TCS receivable (0.5%) | 5 | |
| TDS receivable (0.1%) | 1 | |
| Sales: Amazon | 1,000 |
The gross sale goes in first, then each deduction gets its own line. Book only ₹780 and you understate sales, your GSTR-1 and GSTR-3B totals drift apart, and your TCS and TDS credits go unclaimed.
Where each marketplace keeps its numbers
- Amazon: the settlement (payment) reports in Seller Central. One report can cover many orders and fee types.
- Flipkart: the payment and settlement reports in Seller Hub. Ask each vendor how these get imported.
- Shopify: Shopify Payments payout reports. Good Shopify accounting reconciles gateway fees separately.
- Everyone else: Meesho, Myntra and gateways like Razorpay, Cashfree or PayU each send their own statements.
Cash on delivery, returns and chargebacks
COD money shows up days after dispatch. A return-to-origin order reverses the sale and can carry shipping charges. Chargebacks can land weeks later. Set up a clearing account for COD remittances, a returns ledger and a chargeback ledger, and reconcile all three monthly.
Key Features to Look For in Ecommerce Accounting Software
- Settlement reconciliation that matches each payout to orders, fees and returns.
- One ledger for Amazon, Flipkart and Shopify, not three.
- Inventory costing across every warehouse.
- GST and TDS support: GST TCS, GSTR-1 and 3B, e-invoicing and marketplace TDS credits.
- An audit trail nobody can edit.
- Multi-entity support, if you run more than one company.
- Profit per SKU per channel, after fees, returns and ad spend.
Common Ecommerce Accounting Mistakes to Avoid
- Commission Bookings: Record the gross sale and book commission separately, or your profit figure is wrong.
- Not reconciling TDS & TCS: Match marketplace statements against your tax credit records and the GST portal at least every quarter.
- One ledger per channel: Keep Amazon, Flipkart and Shopify apart so you can see which one actually earns money.
- Using old section numbers: For income from 1 April 2026, refer to the Income-tax Act, 2025. The 1961 Act still governs earlier years.
- Forgetting gateway fees: Razorpay, Cashfree and PayU charges need their own expense line.
How to Switch or Set Up Ecommerce Accounting Software
Review and document your existing process: name your channels, gateways, warehouses and legal entities.
- Choose a cut-off date: Select a cut-off date, cleaning off SKU codes, vendor lists and opening balances from a month or quarter end.
- Map ledgers: set up accounts for each ledger, fee type, and TDS credit, such as Shopify Accounting and Amazon Seller Accounting payouts.
- Connect channels: Test with one month of settlement files.
- Run in parallel: Run both systems for one month-end closing and then reconcile the difference.
- Train and lock controls: assign and maintain audit trail.
Plan for weeks, not days. Budget for data migration, partner fees and training, plus importing your Tally data if that’s where you’re coming from.
People Also Ask:
What’s the top accounting software for online retailers?
For most sellers it’s Zoho Books or TallyPrime. Large multi-entity brands usually look at Oracle NetSuite or SAP Business One, and smaller teams at BUSY or Vyapar. Your pick depends on how many channels you sell on and how complicated your stock is.
Which software suits a small seller who tracks inventory?
BUSY and Vyapar are good places to start. If you expect to grow, Zoho Books with Zoho Inventory gives you more room. Check that batch tracking and multiple warehouses are supported if you need them.
What works best when I sell on several platforms?
Oracle NetSuite for multi-entity brands that want one consolidated ledger, Zoho Books for mid-sized sellers. Connectors vary, so test either one with your own settlement files first.
TallyPrime or Zoho Books for ecommerce?
Pick TallyPrime if your accountant already works in Tally and you care most about compliance reports. Pick Zoho Books if you want a cloud tool with automation and channel connectors. A short pilot with real settlement files will settle it.
What changed under the Income-tax Act, 2025?
The new Act applies from 1 April 2026 and renumbers the old sections. Marketplace TDS, earlier under Section 194O, now falls under Section 393. The rate is 0.1%, same as it has been since 1 October 2024. You still need to match marketplace TDS statements against your books.
Is TDS deducted if my yearly sales are under ₹5 lakh?
Not for resident individuals or HUFs whose gross sales through the marketplace stay within ₹5 lakh a year and who have given their PAN or Aadhaar. Other seller types don’t get this exemption, so check your own case with your CA.
What is GST TCS?
It’s tax the marketplace collects at source on your net taxable sales through it, currently 0.5% in total. The marketplace reports it in GSTR-8. Reconcile it monthly against your GST portal records and claim it through your electronic cash ledger.
How do I record an Amazon or Flipkart settlement?
Book the gross sale first. Then record commission, shipping, returns, GST TCS and TDS as separate lines. Booking only the net payout understates your sales and throws off your GST returns.
Do I need a Shopify integration?
If Shopify is one of your main channels, yes. Payouts, fees and refunds should sync on their own so you’re not rebuilding them by hand.
Conclusion
Most mid-sized Indian sellers will be happy with Zoho Books or TallyPrime. Large multi-entity brands should look at NetSuite or SAP Business One, and lean teams can begin with BUSY or Vyapar. Whichever you choose, book the gross sale, match settlements to orders, reconcile TDS and GST TCS, and keep the audit trail on.
If you’d rather not figure it out alone, Corient helps Indian ecommerce brands choose, set up and run their accounting software, with bookkeeping and compliance support behind it. Get in touch and we’ll help turn your marketplace data into clean, audit-ready books.
