Bookkeeping for E-Commerce & Online Sellers

Marketplaces and processors deposit a net number — gross sales minus fees, refunds, chargebacks, and ad spend, sometimes across several settlement periods. Recording that deposit as revenue understates both sales and expenses, and makes margin impossible to read.

Gross, not net

Platform payouts broken back out into sales, fees, refunds, and chargebacks.

Margin per channel

Revenue reported by platform so you see which channel actually earns.

Nexus watched

Sales tracked by state against each threshold, before you cross one.

COGS that ties

Inventory and cost of goods reconciled across every channel you sell on.

What we handle

Reconciling platform and processor settlements to bank deposits, gross rather than net
Separating merchant fees, refunds, chargebacks, and shipping into their own accounts
Inventory and cost-of-goods-sold tracking across channels
Sales tax tracked by state, including marketplace-facilitator versus seller-collected
Multi-channel revenue reported by platform so you see which channel earns

Common problems we fix

Net deposits booked as revenue, so both sales and fees are understated
No idea which channel or SKU is actually profitable
Nexus triggered in states nobody was tracking

Why your state matters here

Bookkeeping for e-commerce and online sellers is not the same in every state. Sales tax rates and what is taxable, registration and licensing, payroll rules, and filing cadence all vary — and for this industry those differences change real work, not just a number on a form. Pick your state below for specifics.

Trades and specialisms we cover

E-Commerce & Online Sellers is a broad category, and the bookkeeping differs meaningfully between the trades inside it. Here is what actually changes, trade by trade — each is handled under this service rather than as a separate engagement.

Amazon FBA Sellers — jump to this section

Amazon settles on a two-week cycle and the deposit is what remains after referral fees, fulfilment fees, storage, long-term storage surcharges, advertising, refunds, and reimbursements — frequently spanning two settlement periods. The settlement report, not the bank deposit, is the source document, and it has to be broken back out into its component accounts every cycle. Inventory sitting in Amazon warehouses is still your asset and still needs valuing, and reimbursements for lost or damaged stock are neither sales nor a reduction in fees. Sellers who record the deposit as revenue understate sales, understate expenses, and cannot calculate contribution margin on any product.

Shopify Stores — jump to this section

A Shopify store typically runs its own payment processing alongside one or more third-party gateways, each with its own payout timing and fee structure, and each needing separate reconciliation. Unlike a marketplace, you are generally responsible for collecting and remitting your own sales tax on direct sales, which makes the nexus question live rather than academic. Gift cards sold are a liability until redeemed, discount codes need to be visible as a contra-revenue rather than netted into the sale, and app subscriptions accumulate into a real monthly cost that rarely gets categorised.

Etsy Sellers — jump to this section

Etsy deposits net of listing fees, transaction fees, payment processing, offsite advertising fees charged on a percentage of the sale, and shipping label purchases — several of which are debited separately from the payout. Handmade sellers also carry a cost-of-goods problem that platform sellers do not: raw materials bought in bulk and consumed across many items, which needs a sensible allocation method rather than a guess. Offsite ads in particular catch people out, because the fee can arrive on a sale the seller never attributed to advertising.

eBay Sellers — jump to this section

eBay managed payments deposit net of final value fees, insertion fees, store subscription, promoted listing fees, and shipping labels. Sellers running a mix of new inventory and sourced or consigned goods need those separated, because the cost basis works differently — sourced goods carry an acquisition cost per item that only exists if somebody recorded it at the time. Returns are frequent enough in some categories that treating them as a rounding error meaningfully overstates revenue.

Walmart Marketplace Sellers — jump to this section

Walmart settles on its own cycle with referral fees by category and, for sellers using Walmart Fulfillment Services, fulfilment and storage charges alongside. Sellers on both Walmart and Amazon frequently keep one pooled inventory figure across both, which makes cost of goods sold unreliable for either — the fix is channel-level inventory tracking so each marketplace can be evaluated separately. Chargebacks and performance penalties are a real cost line that belongs somewhere visible.

TikTok Shop Sellers — jump to this section

TikTok Shop combines marketplace mechanics with affiliate commission paid to creators on individual sales, which is a cost of sale rather than marketing overhead and behaves quite differently in the accounts. Platform-funded discounts and seller-funded discounts need to be distinguished, because only one of them reduces your revenue. Payout timing is slower than most channels and hold periods are common, so a seller can be profitable and short of cash at the same time — which only shows up in books that track the receivable from the platform.

Dropshipping Businesses — jump to this section

Dropshipping produces high gross revenue against thin margin, and because you never hold stock, there is no inventory account to anchor cost of goods sold — the supplier invoice has to be matched to the order it fulfilled, or margin is unknowable at the product level. Supplier payments in a different currency add exchange differences that need somewhere to go. The tax position is genuinely more complicated than it looks, because the goods ship from somewhere the seller may have no other connection to.

Subscription Box Businesses — jump to this section

A subscription box collects monthly or annually in advance for boxes not yet shipped, which makes deferred revenue central rather than incidental — an annual plan is one month of revenue and eleven months of obligation. Churn and skipped months mean the deferred balance has to be maintained against actual shipments rather than assumed. Component inventory bought in bulk for a specific month’s box is a distinct costing problem, since leftover stock has value only if a future box can use it.

Print-on-Demand Sellers — jump to this section

Print-on-demand has no inventory and a per-unit production cost that is charged only when a sale happens, which makes it one of the few e-commerce models where cost of goods sold is genuinely simple — provided the fulfilment charge is matched to the order rather than treated as a monthly lump. The complication is design royalties and licensing, which are a cost of sale, and running the same designs across several platforms simultaneously, which needs channel-level reporting to show which platform is actually worth the effort.

Wholesale and 3PL Sellers — jump to this section

Sellers moving from direct-to-consumer into wholesale acquire a second business with different terms: invoices with payment terms rather than instant settlement, purchase orders, chargebacks and compliance deductions from retailers, and resale certificates to collect and hold. Third-party logistics adds storage, pick-and-pack, and receiving fees that belong in cost of fulfilment rather than in general overhead, and inventory held at a 3PL still has to be counted and valued.

Not listed? Tell us what you do — these are the ones we are asked about most, not the limit of what we handle.

We keep the books. You run the business.

Categorization, reconciliation, month-end close, and clean financial statements — with nothing left for you to chase.

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How It Works

Free review

We look at how your e-commerce and online sellers books are set up today.

Fix the structure

Chart of accounts rebuilt around how your industry actually earns and spends.

Catch up

Anything behind gets cleaned up at a fixed quoted price.

Close monthly

Current, reconciled books every month — ready for your CPA.

E-Commerce & Online Sellers Bookkeeping by State

Sales tax nexus and taxability, licensing, payroll rules, and filing cadence differ by state. Pick yours for a state-specific guide.

E-Commerce & Online Sellers — Frequently Asked Questions

Do you understand e-commerce and online sellers specifically?

Yes — that is the point of setting the books up by industry. Marketplaces and processors deposit a net number — gross sales minus fees, refunds, chargebacks, and ad spend, sometimes across several settlement periods. Recording that deposit as revenue understates both sales and expenses, and makes margin impossible to read.

What does bookkeeping for e-commerce and online sellers actually involve?

Reconciling platform and processor settlements to bank deposits, gross rather than net; Separating merchant fees, refunds, chargebacks, and shipping into their own accounts; Inventory and cost-of-goods-sold tracking across channels; and 2 other recurring pieces. It is done monthly rather than reconstructed at year end, so the numbers are usable while the decisions are still open.

What usually goes wrong in e-commerce and online sellers books?

The three we see most: net deposits booked as revenue, so both sales and fees are understated; no idea which channel or SKU is actually profitable; nexus triggered in states nobody was tracking. Platform payouts are net of a dozen deductions. Your books need the gross.

Do you work with amazon fba sellers, shopify stores, etsy sellers?

Yes — those are three of the 10 trades covered under this service, and each is listed on this page with what changes about its books. They are handled under one engagement rather than quoted separately.

Do you work in the accounting file my e-commerce and online sellers business already uses?

Yes. We work inside your file so you keep ownership and full visibility. If you do not have one set up yet, we build it around your industry from the start, including a chart of accounts that matches how you actually earn.

Can you clean up e-commerce and online sellers books that are months behind?

That is our specialty. Cleanup is quoted at a fixed price after a short no-obligation review, so you know the cost before any work begins. Scope varies enormously, so we look first and quote second.

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