The biggest difference is how money gets to your bank account. A brick-and-mortar store runs transactions through a POS system, and the daily deposit roughly matches total sales minus credit card processing fees. With e-commerce, platforms like Amazon and Shopify batch payouts on their own schedule, deduct fees before depositing, and lump multiple days of sales into a single transfer. The amount hitting your bank account doesn’t clearly correspond to actual sales, and reconciling those deposits takes real work.

Marketplace fees add another layer. A physical store pays rent, utilities, and credit card processing. An e-commerce seller pays referral fees, fulfillment fees, storage fees, advertising fees, and platform subscription fees. Amazon alone can take 30% or more of a sale price between FBA and referral fees. Each of those fees needs to be categorized correctly so you can see your true margins. If you just record the net deposit as revenue, your financial statements will understate both your top-line sales and your expenses, which makes the numbers misleading for decision-making and taxes.

Sales tax is dramatically more complicated for e-commerce. A brick-and-mortar store typically collects sales tax in one state, maybe one or two jurisdictions. An online seller shipping across state lines can trigger nexus in dozens of states, each with its own rates, filing deadlines, and rules about what’s taxable. Most platforms collect and remit sales tax on your behalf now, but you still need to verify that what the platform collected matches what you owe. Errors happen, and they’re your responsibility.

Returns are another area where the books get messy. E-commerce return rates are significantly higher than in-store returns, sometimes 20% to 30% depending on the product category. Each return needs to be recorded properly. You have to reverse the revenue, account for any restocking or return shipping fees, and update inventory. In a physical store, a return is a quick POS transaction. Online, the refund might process days or weeks later through the platform, making it harder to match up.

Inventory tracking also differs. A brick-and-mortar store has inventory in one location. E-commerce sellers often have stock spread across FBA warehouses, a home warehouse, and possibly a third-party logistics provider. Keeping accurate inventory counts and valuations across multiple locations requires more disciplined tracking. If you sell on multiple platforms simultaneously, overselling becomes a risk that affects both operations and accounting.

None of this means e-commerce bookkeeping is impossible to manage. It just means the systems and processes need to be built for this complexity from the start. Working with a small business accounting firm that understands how platform payouts work, how to properly record gross sales versus net deposits, and how to handle multi-state obligations will save you from a mess that only gets worse the longer it goes unaddressed.