Ecommerce bookkeeping services for Shopify, Amazon, and multi-channel online stores
Sales-channel reconciliation across Shopify, Amazon, Stripe, and PayPal; sales tax nexus tracking; inventory and COGS accounting; merchant-fee and chargeback handling; and per-channel profit dashboards — bookkeeping built for how online stores actually make money.
We work with Shopify, Amazon, Etsy, and multi-channel store owners on the bookkeeping that makes or breaks an ecommerce business: reconciling every payout to the penny, getting inventory and COGS on accrual, tracking sales tax nexus state by state, and surfacing true profit by channel and SKU.
QuickBooks Online · A2X / channel integrations · Gusto · Ramp — professional liability insured — month-to-month, 30-day notice
Pick a time right here — no prep required.
Online stores break the assumptions most bookkeepers work from. The bank deposit isn't your sales number. Inventory isn't an expense when you buy it. Marketplace fees aren't a footnote — they're often your biggest cost line. And sales tax can be owed in twenty states you've never set foot in. We handle every one of these correctly.
What changes with TurnkeyCFO
Every service below is built for how ecommerce businesses actually operate — multiple sales channels, physical inventory, marketplace fees, multi-state sales tax, and razor-thin margins that demand accurate numbers.
Full monthly close for your online store — accurate categorization of channel sales, processing fees, inventory purchases, COGS, advertising spend, software, and overhead. Monthly close package with P&L, balance sheet, and written commentary ready for your review every month, with inventory and COGS reconciled so the numbers actually mean something.
Shopify, Amazon, Stripe, PayPal, Etsy, Walmart — each one pays out gross sales minus its own stack of fees, refunds, reserves, and chargebacks, on its own schedule. We reconcile each channel's gross sales, fees, and net payout, then tie every payout to the matching bank deposit. Your revenue becomes your real revenue, and the gap between "sales" and "what hit the bank" is fully explained.
Post-Wayfair, you can owe sales tax in any state where you cross an economic-nexus threshold — typically $100,000 in sales or 200 transactions — and FBA inventory stored in a warehouse can create physical nexus on top of that. We track your sales by state against each state's threshold so you see where you're approaching or have already triggered a registration and filing obligation, and we keep the books filing-ready for you or your sales tax provider.
Inventory is an asset until it sells, then it becomes COGS. We record inventory purchases to the asset account, recognize COGS as units sell, and capture landed cost — product plus inbound freight, duties, and prep — so gross margin reflects the true cost of each sale. The result: a P&L that stays steady instead of swinging into fake losses every time you restock.
Processor and marketplace fees are a cost of every single sale, not a rounding error to bury in net revenue. We record gross sales and then break out Stripe, PayPal, Shopify Payments, Amazon referral and FBA fees, refunds, and chargeback losses as their own lines. You see exactly what payment processing and disputes are costing you — often a number sellers are shocked by once it's finally visible.
We run payroll for W-2 staff, track every contractor — VAs, designers, photographers, ad agencies, 3PL partners — paid $600 or more for 1099-NEC filing, and collect W-9s before work starts. Accounts payable keeps supplier and inventory bills current; accounts receivable tracks any wholesale or net-terms invoices so money owed to you never slips through the cracks.
Live dashboards that show revenue, fees, and COGS broken out by sales channel and product line — so you can see net margin per channel and per SKU at a glance. Many sellers learn that a channel doing big top-line numbers barely clears a profit after marketplace fees, or that their hero product carries the thinnest margin. You make inventory, pricing, and ad decisions on real margin, not gut feel.
Tax filings and legal matters — coordinated with your CPA or attorney. TurnkeyCFO does not provide tax or legal advice; we keep your books filing-ready and support the process.
The day-to-day realities most bookkeepers have never touched. We have.
The number that hits your bank is net, not revenue.
A $9,400 Shopify payout might represent $10,000 in gross sales, minus $290 in processing fees, minus $310 in refunds — bundling several days of orders into one deposit. Booking the $9,400 as revenue understates your sales and hides your fees and refunds entirely. We split every payout into gross sales, fees, refunds, and chargebacks, then reconcile it to the deposit. This is the single most common ecommerce bookkeeping mistake, and the one that quietly distorts every report you rely on.
One Amazon deposit can net out a dozen fee types.
An Amazon settlement isn't just sales minus a commission. It nets referral fees, FBA fulfillment fees, monthly storage, long-term storage, advertising, refunds, reimbursements, and reserve holdbacks — across a two-week window. Recorded as a single lump deposit, all of that detail disappears. We map each settlement component to the right account so your Amazon channel shows real gross sales and a complete, honest fee breakdown.
Buying stock isn't an expense — selling it is.
Spend $40,000 restocking in March and a cash-basis P&L shows a $40,000 "loss" that month, then phantom profit in the months you sell from that stock. Neither reflects reality. Inventory belongs on the balance sheet as an asset, moving to COGS only as units sell. We keep inventory and COGS on accrual so each month's profit reflects what you actually earned — essential for spotting margin trends, planning reorders, and not panicking over a normal restock.
Your product cost is more than the invoice from the supplier.
A unit's real cost includes the product price plus inbound freight, import duties, customs, and prep or labeling. A product that costs $7 from the supplier might land at $9.50 once freight and duties are spread across the shipment. If COGS only captures the $7, your gross margin is overstated on every sale. We allocate landed cost into inventory so margin reflects what each unit truly cost to get sale-ready.
You can owe sales tax in states you've never visited.
Since the 2018 Wayfair decision, a state can require you to collect and remit sales tax once your sales there cross an economic threshold — commonly $100,000 or 200 transactions a year. Storing FBA inventory in a state can create physical nexus immediately. Sellers routinely trigger nexus in a dozen-plus states without realizing it, accruing back taxes and penalties. We monitor sales by state against thresholds so nexus is a decision you make on time, not a surprise you discover in an audit.
High revenue and high profit are not the same thing.
A marketplace channel can post the biggest top-line number and still be your worst earner once referral and fulfillment fees come out. A bestselling SKU can have the thinnest margin in the catalog. When sales, fees, and COGS are tracked by channel and product, those truths become visible — and you can cut a money-losing channel, reprice a thin-margin product, or shift ad spend toward what actually makes money. Without that breakdown, you're guessing.
Simple, fast, and designed not to take you away from running the store.
We learn your business — which channels you sell on, your inventory and supplier setup, how you handle fulfillment, your current software, and where the numbers feel murky. No sales pitch.
We connect to QuickBooks and your channels, review your chart of accounts, assess how sales and fees are currently recorded, check inventory and COGS treatment, and map your sales-by-state picture before going live.
Monthly close package, reconciled channel payouts, inventory and COGS on accrual, sales tax nexus monitoring, and per-channel profit dashboards running clean from month one.
Your bank deposit is never your sales number. A Shopify payout is gross sales minus processing fees, refunds, and chargebacks, often spanning several days of orders. An Amazon settlement nets out referral fees, FBA fees, storage, and reserves. We reconcile each channel's gross sales, fees, refunds, and net payout separately, then tie every payout to the bank deposit — so your revenue is your real revenue and your fees are visible, not buried.
Almost certainly. After the 2018 Wayfair decision, most states impose economic nexus once you cross a sales or transaction threshold there — commonly $100,000 in sales or 200 transactions. FBA inventory stored in a state can create physical nexus too. We track your sales by state against each state's threshold so you know where you are approaching or have triggered a filing obligation, and we keep the books clean so your sales tax filings or your CPA's work are straightforward.
Inventory is an asset on your balance sheet, not an expense — you only expense it as COGS when it sells. We record inventory purchases to the asset account, recognize COGS as units sell, and account for landed cost (the product plus inbound freight and duties) so your gross margin reflects what each sale truly cost. Without this, your P&L swings wildly: huge losses in months you restock, fake profits in months you sell from existing stock.
Processor and marketplace fees — Stripe, PayPal, Shopify Payments, Amazon referral and FBA fees — are a real cost of every sale and should be recorded as an expense, not netted silently into revenue. Chargebacks reverse the sale and add a dispute fee. We record gross sales, then break out fees, refunds, and chargebacks as their own lines so you can see exactly what processing and disputes are costing you.
Any store carrying inventory should be on accrual for inventory and COGS — cash-basis books make a restock month look like a disaster and a sell-through month look like a windfall, which is useless for decisions and can misstate income. We typically run accrual for inventory and COGS so your monthly profit reflects real performance. Coordinate the tax-reporting method with your CPA.
Yes. We structure the books so revenue, fees, and COGS are tracked by channel — Shopify vs. Amazon vs. wholesale — and build live dashboards so you can see net margin per channel and per product line. Many sellers discover a channel with high revenue is barely profitable after marketplace fees, or that a best-selling SKU has the thinnest margin.
Yes. We run payroll for W-2 staff and track every contractor — VAs, designers, photographers, agencies — paid $600 or more for 1099-NEC filing, collecting W-9s up front. We also handle AP and AR so supplier bills and any wholesale receivables stay current alongside your daily order flow.
Month-to-month engagement, 30-day notice. No multi-year contracts. We keep clients because the work is good, not because paperwork traps them. Use the Instant Estimate to see a real price range before we ever talk.
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