E-Commerce Multi-Channel Accounting: Shopify + Amazon + Wholesale
How to set up your chart of accounts to track profitability by sales channel. Separate Shopify, Amazon, and wholesale revenue, marketplace fees, and per-channel COGS.
The number one question every e-commerce brand owner asks: "Which channel is actually profitable?" If your QuickBooks has one revenue line and one COGS line, you'll never know the answer.
This guide shows you how to structure your chart of accounts so you can see profitability by channel — including the marketplace fees that silently eat your margins.
The Multi-Channel Profitability Problem
Most e-commerce brands sell on multiple platforms: Shopify (your website), Amazon (marketplace), and sometimes wholesale to retailers. Each channel has different:
- Revenue — gross sales before returns
- Returns — return rates vary wildly by channel (Amazon: 15-30%, Shopify: 5-10%)
- Marketplace fees — Amazon charges 8-15% referral fees, Shopify charges payment processing
- Fulfillment costs — FBA fees vs self-fulfillment vs 3PL
- COGS — same product, different landed cost depending on channel
Without separating these by channel, your P&L is useless for decision-making.
Revenue by Channel
Set up separate revenue and returns accounts for each channel:
| Account | Number | Purpose | |---------|--------|---------| | Shopify Sales | 4000 | DTC website revenue | | Shopify Returns & Refunds | 4010 | Contra-revenue for Shopify returns | | Amazon Sales | 4100 | Amazon marketplace revenue | | Amazon Returns & Refunds | 4110 | Contra-revenue for Amazon returns | | Wholesale Revenue | 4200 | B2B retail partner sales | | Wholesale Returns | 4210 | Wholesale returns and allowances | | Shipping Revenue | 4300 | Shipping charges collected |
Marketplace Fees — The Hidden Margin Killer
These are the accounts most e-commerce brands are missing:
- Shopify Platform Fees (6000) — monthly subscription + app fees
- Shopify Payment Processing (6010) — Shopify Payments / Stripe transaction fees (2.9% + 30¢)
- Amazon Referral Fees (6020) — the 8-15% commission on every Amazon sale
- Amazon FBA Storage Fees (6030) — monthly and long-term storage charges
- Amazon Advertising (6040) — PPC and sponsored product spend
When you see these separated out, you might discover that your Amazon channel runs at 5% margin after fees — while Shopify runs at 25%. That changes how you allocate marketing spend.
COGS by Channel
Track product cost separately for each fulfillment path:
- Product Cost - Shopify (5000) — cost of goods for self-fulfilled orders
- Product Cost - Amazon (5010) — cost of goods sent to FBA
- Product Cost - Wholesale (5020) — cost of goods for wholesale orders
- FBA Fulfillment Fees (5210) — Amazon's pick, pack, and ship charges
- Outbound Shipping - Shopify (5200) — your shipping costs for DTC orders
The Channel P&L View
Once set up, you can run a P&L filtered by account range to see each channel's profitability:
Shopify Channel: Revenue (4000-4010) - COGS (5000, 5200) - Fees (6000, 6010) Amazon Channel: Revenue (4100-4110) - COGS (5010, 5210) - Fees (6020-6040) Wholesale Channel: Revenue (4200-4210) - COGS (5020)
This is what lets you make data-driven decisions about where to invest.
Get Started
Our e-commerce chart of accounts template includes all channel-specific accounts pre-configured — Shopify, Amazon, wholesale, marketplace fees, and per-channel COGS. Import it into QuickBooks in 60 seconds.