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Bookkeeping for ecommerce businesses on Shopify, Amazon and Etsy.

Your payout is not your revenue. Our bookkeeping for ecommerce businesses splits every Shopify, Amazon and Stripe payout back into sales, fees, refunds and sales tax, and books inventory and COGS when you sell, so your margin is real. Fixed monthly fees start at $150, and inventory and COGS tracking comes with Scale, from $650.

Fixed monthly fees from $150/monthInventory and COGS on Scale, from $650

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An online seller checking a parcel against an order on her phone

Where online store books usually go wrong.

The same few problems bend most online stores’ numbers. Here is each one, what is really going on, and what we do about it.

  • Shopify sales, payouts and the bank never match

    A payout is net. Fees, refunds and chargebacks come out, sales tax stays in, and it lands days later, often in the next month.

    What we doSplit each payout into sales, shipping, refunds, fees and tax through a clearing account per channel, so every deposit ties to the penny.

  • Gross margin that jumps around every month

    Stock is expensed the day you buy it, so a big restock makes one month look terrible and the next look great.

    What we doKeep stock on the balance sheet as inventory until it sells, and book cost of goods sold from what actually sold.

  • A profit on paper, but no cash in the bank

    The cash went into stock that has not sold yet, ad spend, loan repayments taken from payouts, or owner draws. Profit and cash answer different questions.

    What we doA monthly cash-flow view (part of Scale) that shows where the money went: inventory, ads, loan repayments and draws.

  • Amazon settlement reports that are hard to read

    One settlement mixes sales, referral and FBA fees, storage, ads, refunds, reimbursements and a reserve Amazon holds back.

    What we doBook each line to its own account. The reserve is money Amazon still owes you, so it sits on the balance sheet, not in expenses.

  • No clear answer on sales tax in other states

    Nexus can come from sales into a state or from stock stored there, including Amazon warehouses. Marketplaces collect on their own sales; your own store is yours.

    What we doTrack your sales by state against each state’s threshold every month, and file returns where you are registered.

  • Several channels, and some sales counted twice

    The same order shows up in the channel report, the processor payout and the bank feed.

    What we doRecord every sale once, per channel, with each processor matched to its channel. Then you can see profit by channel.

One deposit. Five numbers inside it.

Booking the deposit as sales is the most common ecommerce bookkeeping mistake. It hides fees, refunds and the state’s sales tax.

We book each part where it belongs, so the profit and loss shows how the store really trades, and the sales tax you owe sits on the balance sheet as a liability.

Shopify guideHow to record Shopify sales in QuickBooksRead the guide

One Shopify payout

Example

What the platform paid you, and what was inside it.

Example: what one Shopify payout contains
Product sales$10,000
Shipping charged$600
Sales tax collected$700
Refunds−$500
Processing fees−$330
Paid to your bank$10,470

Booked properly: net sales of $10,100, fees of $330 as an expense, and $700 of sales tax owed to the state.

  • Shopify stores

    Shopify Payments pays out net of fees and refunds, a few days after the sale, and one payout can cover several days of orders. Gift cards, Shopify Capital and your Shopify bill each need their own treatment too.

    • Each payout cleared through a Shopify clearing account that sits at zero once the deposit lands
    • Gift cards held as a liability until a customer redeems them
    • Shopify Capital recorded as money you owe, not as sales, with the repayments taken from payouts split out
    • Your plan, app and theme charges booked as software costs

  • Amazon and FBA sellers

    Amazon pays on a settlement cycle, usually every two weeks. Each settlement mixes sales, referral and FBA fees, storage, advertising, refunds, reimbursements and a reserve it holds back. Stock in Amazon’s warehouses is still yours, so it still belongs on your balance sheet.

    • Each settlement report booked line by line, so fees, ads and refunds show as their own costs
    • The reserve recorded as money Amazon still owes you
    • Reimbursements for lost or damaged stock set against the inventory they replace
    • FBA stock in transit or in Amazon warehouses counted in your inventory, on Scale

  • Etsy, eBay and other marketplaces

    Etsy and eBay deposit what is left after transaction, listing, payment and ad fees. As marketplaces, they collect and pay the sales tax on your orders in most states, so that tax should never show up as your income. WooCommerce and other channels follow the same method.

    • Deposits split into sales, shipping, refunds and each fee
    • Listing fees and offsite ads on their own lines, so you can see what each channel costs
    • Sales tax the marketplace collected kept out of your sales and your own returns
    • Each platform’s Form 1099-K tied back to your gross sales at year end

Inventory and COGS

Stock you buy is an asset until it sells. Expense it on the day you pay and your margin swings with every restock. We keep inventory on the balance sheet and book cost of goods sold from what actually sold, using your Shopify or inventory app’s figures and your counts.

  • Landed cost: the product plus inbound freight and duties in the cost of each unit
  • Damaged, lost or expired stock written off, with Amazon reimbursements set against it
  • Inventory on the balance sheet tied to your stock report every month
  • Gross margin that reflects the month you sold in

Inventory and COGS tracking and multi-channel reconciliation are part of Scale, from $650/month.

Sales tax across states, and marketplace facilitators

Since a 2018 Supreme Court decision, a state can make you collect its sales tax once your sales into it pass a threshold, commonly $100,000 a year, with no office there. Stock stored in a state, including in Amazon warehouses, can create the duty too. Marketplace facilitator laws make Amazon, Etsy and eBay collect the tax on the orders they process. Sales on your own website stay yours, and some states count your marketplace sales toward your threshold.

  • Sales by state each month, checked against each state’s threshold
  • Marketplace sales and your own-store sales kept apart
  • Sales tax you collect held as a liability, never as income
  • Returns filed where you are registered

Sales-tax filing is part of Growth, from $350/month, and Scale.

What we handle every month.

Everything runs inside your own QuickBooks or Xero for one fixed monthly fee. Each job links to the service that does it. On QuickBooks? See how our QuickBooks Online bookkeeping works.

From $150/month. Inventory, COGS and multi-channel reconciliation are part of Scale, from $650/month.

  • One named contact who knows your file
  • A reply within one business day
  • No long-term contract
See full pricing

Every month, for online sellers

Reports you get each month

  • Profit and loss with gross sales, refunds, net sales, COGS and gross margin
  • Fees, shipping and ad spend as their own lines
  • Balance sheet with inventory, sales tax owed and any Amazon reserve or loan
  • Profit and loss by channel, on Scale
  • Sales by state, checked against thresholds, with returns filed on Growth and Scale
  • Cash-flow report, on Scale

Numbers you can watch: gross margin, refund rate, fees and ad spend as a share of sales, and inventory on hand.

Free books review

What we check in an online store’s books. Free, in about 48 hours.

Add us as your accountant in QuickBooks Online, Xero or the software you use. You get a written list of what is misclassified or unreconciled, and how to fix it. Yours to keep.

  1. Send the form

    Two minutes. Your software, your channels and roughly how busy the file is.

  2. Add us from your own account

    Invite hello@remotebookkeepersllc.com as your accountant in your QuickBooks Online, Xero or other software. We only read the file, and nothing in it changes.

  3. Get your findings

    Within about 48 hours, in plain English.

Get a free books review

No card. No sales call required. Nothing in your books changes.

What we look at in an ecommerce file

  1. Revenue built from depositsSales booked net, with fees, refunds and tax hidden inside.
  2. Clearing accounts that never clearShopify, Amazon, Stripe and PayPal balances that should sit at zero.
  3. Sales tax in the wrong placeSales tax you collected booked as income, not as money owed to the state.
  4. Inventory and COGSStock on the balance sheet, with cost booked from what sold.
  5. Sales counted twiceThe same order recorded from the channel, the processor and the bank.
  6. Loans booked as incomeShopify Capital or other advances recorded as sales, not as a loan.

Fractional CFO for ecommerce.

How much stock to buy, which channel to grow, whether a price still works after fees and ads: those questions need more than a profit and loss.

Our fractional CFO support works from your reconciled books, so the answers rest on real numbers. It covers cash planning around stock orders, margin by channel and the decisions that come with growth, such as a new marketplace or a cash advance offer.

See fractional CFO support

What it covers

  • Cash planned around stock orders and slow months
  • Margin by channel after fees, shipping and ad spend
  • Prices and discounts checked against your real unit cost
  • A second look before you take a loan or a cash advance

Part of Scale, from $650/month, with inventory, multi-channel reconciliation and cash-flow reporting.

Who we work with, and where we stop.

We would rather tell you up front than take on work we cannot do well.

A good fit if you run…

  • A Shopify store
  • An Amazon or FBA business
  • An Etsy, eBay or other marketplace shop
  • A dropshipping store
  • A brand selling on several channels, or a subscription brand selling direct
  • Your books on QuickBooks Online, Xero or other cloud accounting software

Probably not the right fit if you…

  • Want someone to run your stock system, purchase orders or forecasts. We account for inventory; you keep running it.
  • Need customs, tariff or legal advice
  • Only want a once-a-year tax filing with no monthly books
  • Are not ready to keep your books in cloud software

Works with the tools you already use

You keep your apps and your own QuickBooks or Xero file. Nothing to switch, and your data stays yours.

  • Shopify
  • Amazon
  • Etsy
  • Stripe
  • PayPal
  • Square
  • QuickBooks
  • Xero
  • We also work with WooCommerce.

Questions online sellers ask.

Why don’t my Shopify sales match my bank deposits?

Deposits are net of fees, refunds and chargebacks, they include sales tax you collected, and they arrive a few days after the sale, often in the next month. Once each payout is broken into its parts, the sales report and the bank agree.

How do you record Amazon settlements?

Line by line from the settlement report. Product sales and shipping go to income, referral fees, FBA fees, storage and advertising each go to their own cost account, refunds come off sales, and reimbursements are set against the inventory they cover.

The reserve Amazon holds back is money it still owes you, so it sits on the balance sheet. The settlement total then ties to the deposit in your bank, every cycle.

Do you work with Etsy and eBay sellers?

Yes. Each deposit is split into sales, shipping, refunds and fees, and the sales tax the marketplace collected is kept out of your income. If Etsy or eBay is one of several channels, each gets its own clearing account, so you can see profit by channel.

Do you work with dropshipping stores?

Yes. A dropshipping store holds no stock, so there is nothing to count, but each order’s supplier cost still needs to land in the same month as the sale. We match supplier charges to sales, keep app and ad costs on their own lines, and track where your own-site sales create a sales tax duty.

Do I have to collect sales tax in other states?

It depends on where you have nexus. Most states set it by sales into the state, commonly $100,000 a year, and some also count orders, often 200 a year. Stock stored in a state, including in Amazon warehouses, can also create it. Marketplaces such as Amazon and Etsy collect on the orders they process, but sales on your own store are yours.

We track your sales by state every month and file returns where you are registered. Sales-tax filing is part of Growth and Scale.

What is the 1099-K threshold for 2026?

Federally, a payment app or online marketplace sends a Form 1099-K when it pays you more than $20,000 in a year across more than 200 transactions. A 2025 law restored that level after the planned drop to $600. Card processors report payments you take by credit or debit card with no minimum, and some states set a lower threshold.

The form shows gross payments, before refunds and fees, so it is usually higher than the sales in your books. We record gross sales and each deduction separately, so your return ties back to it. More in our guide to the 1099-K threshold for 2026.

Can you catch up months of Shopify or Amazon books?

Yes. We rebuild each month from the platform’s payout and settlement reports, reconcile it to your bank, and fix how inventory and sales tax were booked. Catch-up is quoted as a fixed price before any work starts, then monthly work keeps you current. See catch-up bookkeeping for online stores.

Which plan fits an online store?

Starter (from $150 a month) suits a store with one main sales channel. Growth (from $350) adds payroll, sales-tax filing and tax preparation. Scale (from $650) is built for several channels with inventory: inventory and COGS tracking, multi-channel reconciliation, cash-flow reporting and fractional CFO support.

The exact fee is confirmed after a short look at your volume and complexity. If your volume grows a lot, we talk first, and any change is agreed with you in advance. No long-term contract.

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