E-commerce bookkeeping breaks in predictable ways: sales channels get recorded as one lump deposit, fees disappear into the wrong account, and inventory goes untracked. Here's the setup that avoids all three.
The single most common e-commerce bookkeeping mistake: recording a Stripe or Shopify payout as straight income. A payout is actually gross sales minus fees minus refunds, all bundled together. Recorded as-is, it understates your real revenue and hides how much you're paying in processing fees.
Set up separate accounts for gross sales, processing fees, and refunds, so each payout gets broken into its real components instead of landing as one number.
If you sell on Shopify, Etsy, and Amazon, your chart of accounts should be able to answer "which channel is actually profitable" — not just "how much came in total." That usually means:
QuickBooks Online can track inventory natively on some plans, or you can run inventory through a dedicated e-commerce/inventory app that syncs in. Either is fine — what's not fine is no decision at all, which is how "Cost of Goods Sold" ends up wildly wrong at tax time.
It's tempting to connect every available app to QuickBooks. In practice, each integration is another place data can duplicate or drop. Start with the minimum: your bank, your primary sales channel, and your payment processor — then add more only if a real gap shows up.
Matching a bank deposit to a lump payout isn't real reconciliation for e-commerce. The deposit should tie back to the underlying orders, fees, and refunds for that payout period. This is the step most DIY setups skip — and the one that catches missing sales or double-counted refunds.
Clean e-commerce books tell you which channel to double down on. Messy ones just tell you a number arrived in the bank.
Getting this right once at setup saves months of cleanup later. If your QuickBooks file already feels tangled, a chart-of-accounts review is usually the fastest way back to something trustworthy.