The biggest difference is where the complexity lives. A brick-and-mortar store typically has one point of sale system, collects sales tax in one state, and handles returns across a counter. An e-commerce business might sell through Shopify, Amazon, Walmart Marketplace, and Etsy simultaneously, each with its own payout schedule, fee structure, and reporting format. Getting all of that into your books accurately takes more effort than recording daily register totals.

Sales tax is where things get especially different. A physical store collects tax based on its location. An online seller may owe sales tax in dozens of states depending on where customers live and whether the business has crossed economic nexus thresholds in those states. Every state has its own rules for what triggers a filing obligation. Most e-commerce sellers use tools like TaxJar or Avalara to calculate and remit sales tax, but the bookkeeping still needs to reflect what was collected and what was owed in each jurisdiction.

Platform fees and commissions add another layer. Amazon takes a referral fee, an FBA fee if you use their fulfillment, and storage fees. Shopify charges transaction fees unless you use their payment processor. These aren’t simple credit card processing fees like a brick-and-mortar store pays. They vary by product category, fulfillment method, and sales volume. Recording them correctly matters because they directly affect your true margins.

Revenue recognition works differently too. When a customer buys something on Amazon, you don’t receive that money right away. Amazon batches payouts every two weeks, and those payouts have already had fees, refunds, and adjustments deducted. Your bookkeeping needs to record gross sales, then separately track the fees and refunds so you can see the full picture. If you just book the net deposit amount, you won’t know what you’re actually spending on platform costs.

Shipping and fulfillment costs are a major expense category for e-commerce that barely exists for physical retail. Whether you’re shipping orders yourself, using a third-party logistics provider, or paying for FBA, those costs need to be tracked per channel and ideally per product to understand profitability.

Returns and refunds happen at a higher rate online. In a physical store, a return is a straightforward reversal. In e-commerce, a return might involve restocking fees, return shipping costs, damaged inventory that can’t be resold, and timing differences between when the refund is issued and when the returned product arrives. All of this needs to be recorded accurately or your revenue numbers will be off.

Inventory tracking is important for both types of businesses, but e-commerce adds the complication of inventory sitting in multiple locations. You might have stock in your garage, at a 3PL warehouse, and at an Amazon fulfillment center. Keeping counts accurate across all those locations requires more attention and better systems.

Brick-and-mortar bookkeeping tends to be more straightforward. You have rent, utilities, payroll, inventory purchases, and daily sales. The transactions are fewer and simpler. That doesn’t make it easy, but the data flows through fewer systems with less variation.

For e-commerce sellers, getting this right from the start prevents a mess at tax time. If you’re running an online store and your books are behind or your platform data isn’t flowing into your accounting software properly, working with a bookkeeper in Long Beach who understands the nuances of online selling can save you hours of cleanup and help you actually understand which products and channels are making you money.