Do I need a bookkeeper who specializes in e-commerce?
The short answer is yes, if your e-commerce business has any real volume. Online selling creates accounting situations that general bookkeepers often haven’t encountered and don’t know how to handle correctly.
Sales tax is the biggest reason. E-commerce businesses create nexus in states where they have inventory, significant sales, or marketplace facilitator relationships. Amazon FBA sellers often have nexus in a dozen or more states without realizing it. A general bookkeeper might know your local Arizona sales tax rules but probably isn’t tracking economic nexus thresholds across multiple states or understanding when marketplace facilitators collect on your behalf versus when you’re responsible.
Multi-channel selling creates reconciliation challenges. If you’re selling on Amazon, Shopify, eBay, and maybe doing some wholesale, each platform reports revenue differently, holds funds for different periods, and takes fees at different points. A bookkeeper unfamiliar with e-commerce might book gross sales when the platform shows a payout, miss the fees entirely, or double-count revenue when the same sale shows up in multiple reports.
Inventory accounting matters more than you might think. Knowing your true cost of goods sold requires tracking not just what you paid for products but also inbound shipping, tariffs, Amazon FBA storage fees, and prep costs. Get this wrong and your profit margins are fiction. You might think you’re making money on a product that’s actually losing money once all costs are allocated.
Amazon fees deserve their own mention. FBA fees, referral fees, storage fees, removal fees, advertising spend. Amazon’s settlement reports don’t break these out the way QuickBooks wants to see them. A bookkeeper who hasn’t worked with Amazon sellers before will spend hours trying to make sense of the reports and still probably get it wrong.
Returns and chargebacks need proper handling. E-commerce returns aren’t like retail returns. The timing is different, the fee treatment is different, and inventory adjustments happen at different points. Chargebacks have their own accounting treatment. These transactions need to be recorded correctly or your books don’t reflect reality.
The cost of using a general bookkeeper who doesn’t understand e-commerce usually shows up in three ways. Inaccurate profitability by product or channel. Sales tax compliance problems that surface later as penalties and back taxes. Financial statements that don’t help you make decisions because the numbers don’t reflect how your business actually works.
You might be fine with a general bookkeeper if you’re running a simple Shopify store with sales in one or two states and no inventory complexity. But most e-commerce businesses that have any real traction quickly outgrow what a generalist can handle.
Working with a Scottsdale bookkeeper who understands e-commerce means they already know the platforms, already know the common mistakes, and already have systems for handling the unique challenges. You’re not paying them to learn on your business.
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More Questions
How do I track inventory for my online store?
Connect your sales platforms to accounting software, track cost of goods sold accurately, and reconcile physical counts regularly. The challenge isn't the tracking itself but getting all systems to sync reliably.
Read answerHow do I handle delivery app fees like DoorDash and Uber Eats?
Record the full order amount as revenue and the fees as a separate expense. Don't just book the net deposit or you'll understate both your sales and your deductible expenses.
Read answerHow do I track returns and chargebacks for my online store?
Record returns as revenue reductions and chargebacks as disputed transactions with their associated fees. Keep them in separate accounts so you can see patterns and understand your actual margins.
Read answerHow do I track Amazon FBA fees and refunds in my books?
Amazon deposits a single net amount that bundles sales, fees, refunds, and reimbursements together. You need to break this down using settlement reports or integration software to see what you're actually earning and spending.
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Define billing milestones in your contract, create a schedule of values, and invoice consistently at each project phase. Track retainage separately and record each billing against the specific job in your accounting system.
Read answerWhat's the difference between cash and accrual accounting for online sellers?
Cash accounting records income when you receive payment. Accrual records it when the sale occurs. For online sellers with inventory and delayed marketplace payouts, the difference affects how you see profitability and when you pay taxes.
Read answer