Bookkeeping for eCommerce
eCommerce Bookkeeping Specialists
Multi-channel sales, A2X for Amazon, sales tax nexus by state. We speak online seller.
- AIPB Certified
- QuickBooks ProAdvisor
- Xero Partner
- US-based team
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Selling on three platforms sounds like three revenue streams. In the books, it's three payout schedules, three fee structures, and three different definitions of what counts as "net." Shopify pays out on its own clock. Amazon holds a rolling reserve and nets fees before the money ever touches your bank. Etsy takes its cut a different way again. None of them hand you a number that matches what actually landed in your account, and reconciling that by hand at midnight is how a lot of sellers lose their Sundays.
We work with sellers running a single Shopify store, sellers spread across Shopify, Amazon, and Etsy with a bit of wholesale on the side, and sellers who've crossed enough states to trigger economic nexus and now owe sales tax somewhere they've never set foot. The tools change, usually A2X or Link My Books doing the heavy lifting, but the goal stays the same: books that match your bank account, cost of goods sold that's actually accurate, and sales tax handled state by state instead of guessed at.
Once we're running things, the manual reconciliation stops. Marketplace payouts flow in already broken into sales, fees, refunds, and shipping the way they should be. Nexus gets monitored so a new state doesn't blindside you months later. Inventory and COGS get tracked so your margin is a real number, not a guess based on whatever's left in the bank account after ad spend clears.
Where ecommerce bookkeeping actually helps
- I sell on Shopify, Amazon, and Etsy and none of the payout numbers match what I think I actually madeA2X or Link My Books connected to break every payout into sales, fees, refunds, and shipping, so your books match your bank account down to the cent.
- I have no idea if I owe sales tax in states I've never even shipped a single order fromEconomic nexus monitored against your sales volume and transaction count by state, so you find out before a state notice finds you.
- Amazon and Etsy already collect sales tax on some orders and I don't know if I'm double-counting itMarketplace facilitator collection tracked separately from the tax you're responsible for on your own channels, so nothing gets counted twice.
- My cost of goods sold is basically a guess, just what I paid the supplier, nothing elseLanded cost built from product cost, freight, and duties, so your margin per SKU is a real number you can actually price against.
- Inventory sitting across three Amazon fulfillment centers and I've genuinely lost track of what I ownInventory reconciled against your platform reports monthly, so what's on the books matches what's on the shelf.
What's different about ecommerce bookkeeping
- Multi-channel reconciliation across Shopify, Amazon, Etsy, and wholesale, via A2X or Link My Books
- State-by-state economic sales tax nexus monitoring as your revenue grows
- Marketplace facilitator tax tracking, separating what Amazon or Etsy already collected from what you owe directly
- Cost of goods sold built from landed cost: product, freight, and duties
- Inventory reconciliation across fulfillment centers and warehouses
- Ad spend and platform fees coded correctly, not lumped into one mystery expense line
- Quarterly books kept tax-ready ahead of the estimated tax deadline
Where ecommerce books usually go sideways
The files we take over most often share the same three problems. Marketplace payouts booked as one lump deposit instead of broken into sales, fees, and refunds, which makes the P&L technically balance but tell you nothing about real margin. Sales tax nexus never checked as revenue crossed state thresholds, so a seller finds out they owe back tax in a state they've never visited, sometimes years after the fact. And cost of goods sold estimated off supplier invoices alone, ignoring freight and duties, which quietly overstates margin on every single sale.
Each of those gets sorted at onboarding. A2X or Link My Books gets connected so every payout arrives already itemized. Nexus gets checked against your actual sales by state, not just your headquarters address. Landed cost gets built into your product costing so COGS reflects what a unit actually cost to get to a customer, freight and duties included.
From there it runs quietly in the background. Monthly reconciliation catches drift before it becomes a real discrepancy. Nexus gets rechecked as revenue grows, so a new state gets flagged before it becomes a compliance problem instead of after. And the monthly P&L finally tells you something useful: which channel is actually profitable and which one is just busy.
"Shopify, Etsy, Amazon, plus a bit of wholesale on the side. I was reconciling Stripe payouts manually at midnight every Sunday. They set up A2X and now it just runs. I sleep on Sundays."
What's included
- Multi-channel payout reconciliation (Shopify, Amazon, Etsy, wholesale) via A2X or Link My Books
- State-by-state sales tax nexus tracking as revenue grows
- Marketplace facilitator tax reconciliation
- COGS and landed cost tracking by product
- Inventory reconciliation across channels and fulfillment centers
- Ad spend and platform fee categorization
- Monthly profit and loss with channel-by-channel breakdown
- Year-end handover to your CPA or EA
Why ecommerce sellers pick us
We run multi-channel books every day
Shopify, Amazon, Etsy, wholesale. Different payout logic, different fee structures. We reconcile all of it, not just the easy channel.
Nexus tracked state by state
Your sales volume and transaction count get checked against economic nexus thresholds as they grow, so a new state gets caught early, not after a notice arrives.
COGS that's actually accurate
Landed cost built from product, freight, and duties, not just the supplier invoice. Your margin per SKU means something.
Inventory that matches the shelf
Reconciled monthly against platform and fulfillment reports, so what the books say and what you actually hold line up.
Margin visible by channel
The monthly P&L breaks out revenue and cost by channel, so you can see which platform is actually earning and which is just moving inventory.
A2X and Link My Books, set up properly
Connected and mapped correctly from day one, so every payout lands in the right accounts instead of one messy deposit line.
Get your channels reconciled to the cent
Tell us which platforms you sell on and roughly your monthly order volume. Quote in writing the same business day.
Three seller shapes
One Shopify store, scaling steadily
A single store, one payment processor, growing order volume. Books are simple enough to run lean but the seller has outgrown doing it themselves between fulfillment runs.
What changes
- Shopify and Stripe payouts reconciled monthly
- COGS tracked per product from day one
- Sales tax registered where nexus applies
- Clean monthly P&L for the first time
How online sellers typically handle their books
DIY spreadsheet Early-stage seller | Generalist bookkeeper Not ecommerce-specific | Ecommerce-focused (us) Multi-channel, nexus, COGS | |
|---|---|---|---|
Multi-channel payouts reconciled to the cent | No | Partial | Yes |
Sales tax nexus tracked by state | No | No | Yes |
COGS includes freight and duties | No | Partial | Yes |
Inventory reconciled to platform reports | No | No | Yes |
Margin visible by sales channel | No | Partial | Yes |
Books reviewed by an AIPB-certified bookkeeper | No | No | Yes |
Sundays free of manual reconciliation | No | Partial | Yes |
How we price ecommerce bookkeeping
Ecommerce bookkeeping pricing depends on how many channels you sell through, monthly order volume, and how many states your nexus tracking needs to cover. A single-channel store doing a few hundred orders a month is a very different scope than a multi-channel seller crossing nexus in a dozen states.
Fill in the quote form, tell us your channels and rough order volume, and we'll come back with a written number the same business day. If your books need catch-up work before we take over, that's quoted separately so the two numbers are clear.
What clients say
"Shopify, Etsy, Amazon, plus a bit of wholesale on the side. I was reconciling Stripe payouts manually at midnight every Sunday. They set up A2X and now it just runs. I sleep on Sundays."
eCommerce bookkeeping FAQ
Two things to remember
Every account is reconciled and kept tax-ready by an AIPB-certified bookkeeper. Every account is run inside the US. Those two anchors shape how we handle compliance for ecommerce sellers specifically.
Services we provide
Service
Xero Bookkeeping
Setup, migration, and day-to-day bookkeeping in Xero.
Service
Virtual Bookkeeping
Cloud-first for eCommerce, SaaS, agencies. A2X, Link My Books, Stripe, Dext wired in.
Service
Outsourced Bookkeeping
Full delegation, compliance-heavy. Contractors, hospitality, construction, allied health. AIPB certified.
Sleep on Sundays again.
Tell us your channels and order volume. We'll quote your retainer the same day.