Expert verified Unlike traditional businesses, ecommerce sellers face unique challenges. This is why opting for ecommerce accounting and bookkeeping services becomes essential.
Understand who needs it and why and how to find the best ecommerce accounting and bookkeeping services near you.
Ecommerce Accounting and Bookkeeping Services: Who Needs It and When
Ecommerce accounting refers to the systematic process of recording, tracking, and analyzing the financial activities of an online business. This includes revenue recognition, cost of goods sold (COGS), taxes, and profit calculations.
Bookkeeping, forms the basis of accounting, and involves daily recording of transactions like:
- Sales across platforms (Amazon, Flipkart, Shopify, etc.)
- Payment gateway settlements (Razorpay, Paytm, Cashfree, etc.)
- Returns and chargebacks
- Marketplace fees and commissions
- Inventory purchases and stock movement
- Taxes: GST, TDS, TCS
Who Needs Ecommerce Accounting and Bookkeeping Services?
1. Startup Ecommerce Businesses
Mistakes in GST setup or expense tracking can lead to future compliance issues.
Needs:
- GST registration & chart of accounts setup
- Ecommerce-focused software selection (e.g., Zoho Books, ProfitBooks)
2. Growing Sellers (100+ Monthly Orders)
As sales increase, manual tracking becomes error-prone and time-consuming.
Needs:
- Automated bookkeeping
- Monthly GST filing & reconciliation
- Platform-wise reports
- Returns & fee tracking
3. Multi-Channel or High-Volume Sellers
Multiple platforms create complex settlements, TCS rules, and reporting chaos.
Needs:
- Multi-platform reconciliation
- Inventory sync across channels
- Chargeback and return management
4. International Ecommerce Sellers
Cross-border sales involve handling forex, GST on exports, and global taxes.
Needs:
- Forex accounting
- Export documentation & LUT filing
- GST refund claims
- Support for Etsy, eBay, Shopify Global
5. Inventory-Heavy Businesses
Without proper inventory accounting, COGS and demand forecasting suffer.
Needs:
- Integrated inventory-accounting tools
- Real-time COGS tracking
- SKU-level profit analysis
6. Sellers Preparing for Funding or Loans
Investors and banks need clean, audit-ready financials.
Needs:
- P&L and balance sheet preparation
- Books as per Companies Act
- Budgeting & forecasting
7. Cash Flow–Struggling Businesses
High sales don’t guarantee healthy cash flow without financial control.
Needs:
- Cash flow tracking
- Expense control
- Reconciliation of bank & gateways
When Do You Need Ecommerce Accounting Services?
1. At Business Launch: If you’re just starting out,this is the ideal time to get basic accounting services including:
- GST registration
- Setting up your accounting system
- Organizing your chart of accounts correctly from the beginning
2. Before GST Filing Deadlines: When it’s time to file your GST returns and you’re dealing with data spread across different platforms, it’s time to seek help. Recommended services include
- GST return filing
- TCS (Tax Collected at Source) reconciliation
- Input credit tracking to ensure compliance and accuracy.
3. During the Growth Phase: Unclear product profitability, marketplace payout discrepancies, and outdated reports are common challenges for growing businesses. At this stage,these services become essential:
- Automated bookkeeping
- Regular profit & loss statements
- Marketplace fee tracking
4. Facing Cash Flow Issues: Even with strong sales, if you’re experiencing tight cash flow or getting hit with unexpected tax bills, you need better financial visibility. Services that assist:
- Cash flow forecasting
- Management accounting,
- Real-time financial dashboards
5. Preparing for Funding or Audit: When you’re getting ready to pitch to investors or prepare for an audit, your books need to be spotless and professional. You’ll need
- Clean financial statements
- Up-to-date balance sheets,
- Investor-ready reports or decks
6. Expanding to New Channels or Markets: If you’re adding a Shopify or direct-to-consumer (D2C) store or beginning to sell internationally, your accounting needs will change. Look for:
- Multi-currency accounting
- Channel-based tracking
- International tax compliance services
7. Inventory Mismanagement: If you’re dealing with overstocking, dead stock, or you’re unsure about your true COGS, it’s time to integrate accounting with your inventory management. Services needed:
- Inventory accounting integration
- Automated reorder points,
- Proper valuation methods
What Ecommerce Accounting & Bookkeeping Services Cover?
Here’s a look at the most essential ecommerce accounting and bookkeeping services every online seller in India should know about:
Sales Recording & Marketplace Reconciliation
- Recording sales, returns, and refunds from platforms like Amazon, Flipkart, Shopify, Nykaa, etc.
- Reconciling settlement reports with bank deposits.
- Identifying discrepancies such as short payments, incorrect deductions, or hidden fees.
Accurate reconciliation ensures you’re receiving the full payment you’re owed and provides transparency into platform-specific deductions like commissions, TCS, and shipping charges.
GST Compliance & Filing
- GST registration (if not already done)
- Filing of GSTR-1 and GSTR-3B returns
- TCS (Tax Collected at Source) reconciliation from marketplaces
- ITC (Input Tax Credit) reconciliation with GSTR-2B
- Advisory on GST applicability based on sales location (inter/intra-state)
- E-way bill generation for logistics compliance
Non-compliance can result in penalties, blocked ITC claims, and disruptions in cash flow. Proper GST filing ensures you’re claiming all eligible credits and staying audit-ready.
Inventory Management & Accounting
- Real-time tracking of stock across warehouses or fulfillment centers (e.g., Amazon FBA)
- Calculating Cost of Goods Sold (COGS)
- Inventory valuation using FIFO or Weighted Average methods
- Flagging slow-moving or deadstock items
Proper inventory accounting improves cash flow, reduces holding costs, and enhances profitability analysis at the product or SKU level.
Expense Tracking & Categorization
- Recording operating expenses such as packaging, logistics, advertising, software subscriptions, and salaries.
- Linking ad spend (Meta Ads, Google Ads, Amazon Ads) to revenue for ROI analysis
- Categorizing fixed vs variable costs
Detailed expense tracking helps identify profit-draining areas and optimizes resource allocation
Financial Reporting & Analysis
- Profit & Loss (P&L) statements
- Balance Sheet
- Cash Flow Statements
- Custom dashboards showing channel-wise profitability, CAC (Customer Acquisition Cost), ROAS (Return on Ad Spend), and LTV (Customer Lifetime Value)
These reports help business owners make data-driven decisions, track performance, and prepare for investor discussions or bank loans.
General Bookkeeping & Accounts Maintenance
- Recording all financial transactions
- Maintaining a clean general ledger
- Reconciling bank and credit card statements
- Managing accounts receivable and payable
Ensures reliable financial data, which is essential for tax filing, compliance, and strategic planning.
Income Tax & TDS Compliance
- Filing Income Tax Returns (ITR) for businesses (Proprietorship, Partnership, LLP, or Pvt Ltd).
- TDS management for vendor payments, commissions, professional fees, etc.
- Guidance on Presumptive Taxation under Section 44AD (for eligible businesses).
- Strategic tax planning to legally minimize tax liability.
Correct and timely income tax filings reduce legal risks and help you claim eligible deductions to save tax.
Payroll Processing & Statutory Compliance
- Salary processing and payslip generation
- PF, ESI, and Professional Tax compliance
- TDS on salaries
- Employee expense reimbursements
Essential for businesses with in-house teams or warehouse staff to stay compliant with labor laws and payroll regulations.
Platform-Specific Accounting Services
Each ecommerce platform has unique fee structures, tax deductions, and reporting formats. Expert services handle:
- Amazon: FBA fees, storage charges, returns reconciliation, TCS.
- Flipkart: Commission fees, promotions, GST credits.
- Shopify / D2C Brands: Payment gateway reconciliation (e.g., Razorpay, PayU), manual refund tracking.
- International Sales: Handling forex conversions, customs duties, and IGST.
Marketplace-specific deductions can erode margins if not carefully tracked and reconciled.
Automation & Software Integration
- Accounting Software: Zoho Books, ProfitBooks, TallyPrime
- Ecommerce Integrations: Webgility, ProfitBooks, ClearTax, Giddh
- Payment Gateway Syncs: Razorpay, Paytm, Cashfree, Stripe
Reduces manual effort, increases accuracy, and enables real-time financial tracking across platforms.
Financial Forecasting & Strategic Advisory
- Budgeting and financial goal-setting
- Cash flow forecasting
- Fundraising support and investor-ready financials
- Tax-saving strategies
Proactive financial planning enables sustainable growth and prepares the business for scale or investment rounds.
Choose the Right Ecommerce Accounting & Bookkeeping Services: Looking Beyond the Basics
Selecting the right ecommerce accounting partner is not merely about looking into years and experience.
Here’s a framework to help you choose the right partner:
Understanding of Marketplace Algorithms
Amazon, Flipkart, and Meesho don’t just take commissions, they deduct fees in complicated ways. A traditional accountant may miss hidden charges and late payments.
Choose a provider who can decode marketplace reports and spot revenue leakages you wouldn’t notice on your own.
Tech Backed Expert Services
Purely manual bookkeeping is outdated and purely automated “AI bookkeeping apps” also fail when confronted with messy Indian GST rules.
The best service is a blend of automation for speed, humans for judgment. This balance saves money without creating errors during reconciliations.
Assess Problem-Solving With a Sample Report
Don’t just ask the provider for a proposal, give them a messy Amazon settlement report or Flipkart reconciliation file and see how they handle it.
This “stress test” reveals who’s just talking versus who can actually fix ecommerce-specific accounting chaos.
Global Sales Readiness
Even if you’re not selling internationally yet, you may. Your accountant should be ready. Cross-border sales add complexity.
Start with someone who can scale into it with you. Assess their experience with international payment systems, FX conversion, multi-currency books, GST exemption for exports, and FEMA compliance
Reporting That Drives Decisions
Don’t settle for a GST return and basic P&L. Your accountant should help you run your business better with elaborate and actionable insights.
Great reporting reveals hidden profit opportunities and helps plan inventory, marketing, and expansion intelligently.
Cash Flow Fluency for Ecommerce
Cash flow issues kill more ecommerce businesses than competition. Your accountant must help you plan and protect liquidity.
Look for providers with clear tracking of marketplace payout cycles and forecasting based on sales peaks and return trends.
Seamless Scalability
Don’t hire for ₹80K/month revenue. Hire for ₹80Lakh/month readiness. If your accountant can’t scale, you’ll face disruption just when you’re hitting traction.
Find service providers with tiered pricing models that grow with your business and have tech systems that can handle thousands of orders/day.
Top Benefits of Outsourcing Ecommerce Accounting to PKC
PKC is one of the leading providers of ecommerce accounting services. Working with us you can benefits:
Automated Data Sync Across Platforms
PKC connects directly to your sales platforms, like Amazon and Shopify, and payment gateways. This automates your entire data flow, eliminating manual entry and human error.
Error-Free GST & TCS Compliance
Our accountants specialize in e-commerce taxation, handling complex GST filings and TCS reconciliations. We ensure you correctly claim input tax credit and avoid costly, platform-specific errors.
SKU-Level Inventory & Profitability Analysis
It’s not enough to know overall profits, we at PKC track profitability down to each product. We provide insights on true costs, margins, and dead stock to help you make smarter business decisions.
Actionable Insights, Not Just Reports
We don’t just send spreadsheets; we turn your numbers into strategic recommendations. We offer monthly review calls and dashboards to help you with pricing, ad spend, and cash flow.
Audit & Funding-Ready Books
We ensure your books are always clean and standardized for audits and investors. We support due diligence and funding rounds to ensure there are no last-minute surprises.
Scalable Support
Whether you’re a small business or a large enterprise, our systems and team scale with you. Our support evolves with your business, so you never need to switch accountants as you grow.
Multi-Currency & Global Sales Support
Selling internationally? We can handle forex, Stripe/PayPal accounting, and cross-border compliance with ease.
Cash Flow Forecasting
PKC tracks the delay between sales and settlements, helping you avoid liquidity crunches during return-heavy periods or sale seasons.
Personalized Service & Rapid Response
A dedicated team ensures query resolution within 48 hours, backed by a structured communication workflow.
Integrated Business Consulting
Beyond accounting, PKC offers process improvement, tax structuring, and strategic finance consulting, a true full-stack financial partner.
FAQs About Ecommerce Accounting and Bookkeeping Services India
Yes. Even small sellers on Amazon, Flipkart, or Shopify must comply with GST and TDS rules. Proper bookkeeping prevents errors and avoids penalties.
Costs vary based on the size of your business and complexity. Small sellers may spend a few thousand rupees monthly, while larger businesses pay more for advanced services.
Outsourcing gives you access to experts at a lower cost than hiring full-time staff. It also ensures accuracy, compliance, and valuable insights for growth.
