How do I track fees from Shopify, Amazon, and PayPal?
The biggest mistake is recording only what hits your bank account. When you sell $500 worth of products and receive a $462 deposit, your books need to show $500 in revenue and $38 in fees. Recording just the $462 understates your actual sales and hides what you’re really paying these platforms.
Each platform provides reports that break down exactly what happened. Shopify has payout reports under Settings that show gross sales, refunds, and fees for each payout cycle. Amazon Seller Central has Settlement Reports that detail every referral fee, FBA fee, and storage charge. PayPal transaction reports show the fee taken from each payment.
Create separate expense accounts for platform fees. At minimum, have one account for payment processing fees and another for marketplace fees. Some businesses break it down further by platform. The right level of detail depends on how much you’re selling and whether you need to compare costs across channels.
When you record a payout, the entry should debit your bank account for the deposit amount, debit your fee expense account for the fees withheld, and credit revenue for the gross sale amount. This keeps your books accurate and ensures you’re capturing every fee as a deductible expense.
If you’re processing significant volume, apps like A2X, Synder, or Link My Books connect your platforms directly to QuickBooks and automate this breakdown. They pull settlement data and create the proper journal entries with gross sales and itemized fees. The monthly cost usually pays for itself in time saved and accuracy gained once you’re past a few hundred transactions per month.
Reconcile on the same schedule as your payouts. Shopify and PayPal typically pay out daily or weekly. Amazon settles every two weeks. Match your fee tracking to that rhythm so you’re not trying to reconstruct months of transactions at once.
The fees add up faster than most e-commerce sellers expect. Between payment processing, referral fees, fulfillment charges, and subscription costs, you might be paying 15% to 30% of gross revenue to these platforms. Tracking fees properly is the only way to know your real margins and make informed decisions about which channels are actually profitable.
If your current books just show net deposits without the fee breakdown, a Richmond bookkeeper can help you set up the right account structure and either configure automation tools or establish a manual process that captures everything correctly going forward.
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