The default chart of accounts in QuickBooks Online wasn’t built for e-commerce. It gives you generic categories like “Sales” and “Advertising” that don’t capture what’s actually happening in your business. An e-commerce business needs accounts structured around sales channels, marketplace fees, and inventory movement or the reports won’t tell you anything useful.

For income accounts, separate your revenue by channel. Create individual income accounts for Amazon Sales, Shopify Sales, Walmart Sales, or whatever platforms you sell on. You also want a Shipping Income account if you charge customers for shipping. Refunds and returns should be tracked as a contra-revenue account (something like Sales Returns and Allowances) rather than buried in expenses. This keeps your gross revenue accurate and lets you see your true return rate.

Cost of goods sold is where most e-commerce sellers get it wrong. You need accounts for Product Cost (what you actually paid for inventory), Shipping to Customers, Packaging and Supplies, and Marketplace Fees. Amazon seller fees, Shopify transaction fees, and payment processing fees all belong in COGS because they’re directly tied to generating revenue. Lumping them into general expenses makes your gross margin look better than it really is, which leads to bad pricing decisions.

For operating expenses, think about what you actually spend money on. Advertising should be broken out by channel so you can see what you’re spending on Amazon PPC versus Facebook ads versus Google Shopping. Other common accounts include Software and Subscriptions (for tools like inventory management or listing software), Storage and Warehousing (or FBA storage fees if you use Fulfillment by Amazon), and Office Supplies.

On the balance sheet side, your Inventory asset account is critical. If you’re selling physical products, inventory needs to be tracked as an asset that converts to COGS when sold. You’ll also want an account for Marketplace Payables or Funds in Transit to capture money that platforms owe you but haven’t deposited yet. Amazon and Shopify don’t pay you instantly, and that timing gap needs to be reflected in your books. Sales Tax Payable is another important liability account since e-commerce sellers often have nexus in multiple states.

Keep the chart of accounts as lean as possible. You don’t need 15 sub-accounts under office expenses, but you do need enough detail to answer the questions that matter. Which channel is most profitable? What’s my true cost per unit after fees and shipping? Are my ad costs actually generating enough margin to justify the spend?

If you’re not sure how to configure this in QuickBooks Online, getting the setup right from the start saves you from reclassifying hundreds of transactions later. Our bilingual bookkeeping services include QuickBooks configuration specifically for how your business operates so your chart of accounts actually reflects what you need to track, not just what came preloaded.