Why your ecommerce chart of accounts matters
Your ecommerce chart of accounts is the foundation of every financial report you generate.
It determines how transactions are categorized, how revenue and expenses flow through your books, and how much visibility you have into the actual performance of your business.
Suggested read: Scalable QuickBooks Chart of Accounts for Ecommerce Growth
What makes an ecommerce chart of accounts different
Every transaction carries layers of complexity that generic accounting structures cannot handle. An ecommerce chart of accounts must capture nuances that simply do not exist in traditional retail.
Multiple revenue streams with different behaviors
A brick-and-mortar store has one point of sale. An ecommerce business might sell through Shopify, Amazon, eBay, Walmart, Etsy, and a wholesale channel simultaneously.
Each platform pays out differently, reports differently, and charges different fees.
Your ecommerce chart of accounts needs separate revenue accounts for each channel. Without that separation, you cannot answer basic questions like which marketplace drives the most profit or whether your direct-to-consumer site outperforms your Amazon storefront after fees.
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Fees embedded in every transaction
Marketplace selling comes with a fee structure that traditional retail does not face:
- Referral fees and commissions that vary by category and platform
- Payment processing fees from Stripe, PayPal, or Shop Pay
- Fulfillment fees for FBA or third-party logistics providers
- Advertising costs tied directly to product sales
- Subscription fees for seller accounts and software tools
A properly structured ecommerce chart of accounts breaks out each fee type so you can see exactly how much it costs to sell on each channel.
Shipping as both revenue and expense
Shipping in ecommerce plays a dual role. You may charge customers for shipping, creating a revenue line item.
You also pay carriers to deliver those orders, creating an expense. And when shipping is free to the customer, you absorb the full cost as a margin reduction.
A standard chart of accounts typically includes one shipping expense category. An ecommerce chart of accounts requires more granularity:
- Inbound freight for inventory received from suppliers
- Outbound shipping for customer orders
- Shipping revenue collected from customers
- Carrier-specific expense accounts for rate comparison
This structure lets you calculate true shipping margin and identify whether your free shipping threshold actually makes financial sense.
Returns and refunds at scale
Returns are a cost of doing business in ecommerce, especially in apparel and consumer electronics. A single return triggers multiple accounting entries: revenue reversal, inventory adjustment, potential restocking fees, and return shipping costs.
Without dedicated accounts for returns, refunds, and chargebacks, these transactions get buried in your revenue and expense lines. Your top-line sales look artificially high, and your true net revenue remains unclear.
A well-designed ecommerce chart of accounts includes contra-revenue accounts for returns and refunds, plus expense accounts for restocking labor and return shipping.
Inventory complexity across locations
Traditional retail tracks inventory in one location.
Ecommerce sellers often hold stock in multiple warehouses, FBA fulfillment centers, and retail locations. Each location may have different carrying costs, shrinkage rates, and turnover speeds.
Your ecommerce chart of accounts should support inventory tracking by location or at least by fulfillment method. This distinction matters when calculating landed cost, managing COGS, and understanding which inventory channels perform best.
Payouts that do not match sales
Marketplaces do not pay you when a sale occurs. They batch transactions, deduct fees, hold reserves, and release funds on their own schedule.
A single payout might include sales from two weeks ago, minus refunds from last month, minus fees you never saw itemized.
Reconciling these payouts requires an ecommerce chart of accounts that distinguishes between sales recorded and cash received. Without that separation, your books will never match your bank statements, and month-end close becomes an exercise in frustration.
5 must-have accounts every multichannel seller needs
A few key accounts make the difference between clarity and confusion.
1. Channel-specific revenue
Track sales separately for each platform (e.g., Amazon Sales, Shopify Sales). This reveals which channels are truly profitable after fees.
For example, Amazon may drive 60% of volume but at a 12% fee rate, while Shopify is 30% of sales at just 2% processing cost.
2. Payment processor balances
Use asset accounts for PayPal, Stripe, and Shopify Payments. When a customer pays today but the processor deposits funds later, these accounts keep your cash position accurate.
3. Platform fees and commissions
Track fees by type and channel (e.g., Amazon Referral Fees, Shopify Payment Fees). This level of detail exposes trends, such as rising FBA fees or shifting product mix.
4. Shipping and fulfillment expenses
Separate accounts for FBA Fulfillment, 3PL Shipping, and direct carrier costs reveal the true cost of fulfillment by channel and method.
5. Returns and refunds by channel
Track returns and refunds separately for each channel (e.g., Amazon Returns, Shopify Returns). This preserves cost of goods sold accuracy and highlights operational or quality issues.
As your business adds new channels, these accounts must scale with you.
Here is how to build and document your ecommerce chart of accounts for growth.
Suggested read: How to Conquer Ecommerce With a Growth Mindset
Step-by-step: Setting up your ecommerce chart of accounts
A stepwise process ensures your ecommerce chart of accounts is accurate from day one.
- Export or review your current COA: If you use QuickBooks, Xero, or another system, export your COA and review for clarity. Identify gaps, such as missing channels or fee types.
- Map revenue streams by channel: List every sales channel (Shopify, Amazon, eBay, etc.) and create a revenue account for each. Avoid merging channels; each has unique fees and payment timing.
- Add expense categories for fees, shipping, and returns: For each channel, list all fees and create separate accounts (e.g., Amazon Referral Fees, Shopify Payment Fees). Add shipping and ecommerce fulfillment accounts for each method, and returns accounts for each channel.
- Create sub-accounts for payment processors and marketplaces: Set up asset accounts for PayPal, Stripe, and Shopify Payments. This ensures accurate tracking of funds held before deposit.
- Assign account numbers and document naming conventions: Use consistent numbering (e.g., 4100 for Amazon, 4200 for Shopify) and document your conventions. This prevents confusion as you grow.
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Automating COA setup and maintenance
Accounting integrations like Webgility can:
- Auto-create and sync accounts for each channel
- Map fees and payouts automatically
- Flag mismatches or missing accounts in real time
For example, Webgility syncs orders, fees, and payouts from every channel directly to the right accounts in QuickBooks, eliminating manual entry and errors. Businesses using Webgility save up to 90% of reconciliation time.
Building your COA is just the start. Keeping it optimized is what drives long-term value.
Best practices for maintaining and optimizing your chart of accounts
Your ecommerce chart of accounts is a living system. Here is how to maintain and optimize it as your business evolves.
1. Review your COA quarterly (or after major changes)
Triggers include adding a new sales channel, changes in fee structures, or hitting revenue milestones. Look for unused accounts, overstuffed categories, or misnamed accounts.
2. Adjust your COA when you expand
When you add a channel like Amazon, create “Amazon Revenue” and “Amazon Fees” accounts. Integrations can auto-create these accounts to maintain consistency.
Suggested read: An Ecommerce Business Owner's Guide to FBA Spending
3. Keep documentation and assign ownership
Maintain an internal COA guide and assign a team member to approve changes. Use audit logs to track all updates.
With Webgility, unused accounts are flagged, new channels are auto-mapped, and audit trails show every change. Real-time sync and exception alerts ensure your COA stays accurate as complexity grows.
For many, ecommerce automation is the only way to keep a COA accurate as complexity grows.
Suggested read: The Complete Guide to Ecommerce Accounting
How Webgility helps: Automation for your ecommerce chart of accounts
Building the right account structure is only half the challenge.
The other half is getting transaction data into those accounts accurately and consistently, without hours of manual entry.
Webgility connects your sales channels directly to your accounting software and posts every order, fee, refund, and payout to the correct accounts automatically. Your ecommerce chart of accounts becomes a living system that updates in real time.
What Webgility automates:
- Fee mapping: Captures referral fees, FBA costs, payment processing fees, and commissions at the transaction level and posts each to the right expense account
- Order-level posting: Posts orders with full detail, including line items, taxes, discounts, and shipping, so your ecommerce chart of accounts reflects true revenue by channel
- Payout reconciliation: Imports settlement data and matches payouts to orders and fees, keeping your books balanced
- Real-time sync: Updates inventory and financials across Shopify, Amazon, eBay, Walmart, and other channels as transactions occur
- SKU-level insights: Tracks revenue, COGS, and fees by product so you can see which SKUs generate margin
Schedule a demo with Webgility today.
Frequently asked questions (FAQs)
Can I use a default COA template for ecommerce?
Default templates miss key ecommerce needs like channel-specific revenue, payment processor balances, and platform fees. Customizing your COA is essential for accurate tracking.
How do I handle new sales channels or payment methods?
Add new revenue and fee accounts for each channel or payment method. Automation tools like Webgility can auto-create and map these accounts as you expand.
What if I make a mistake in my COA?
Most accounting systems allow you to edit or merge accounts. With automation, changes are tracked in audit logs, making corrections easy.
How do automation tools help with COA management?
Integrations like Webgility sync orders, fees, and payouts directly to the right accounts, flag mismatches, and keep your COA current as your business grows.
February 23, 2026
5 min read
David Seth
David Seth
