GUIDE · BOOKKEEPING FOR ECOMMERCE
Bookkeeping for ecommerce,
from the payout back to the sale.
Bookkeeping for an online store means turning each platform payout back into the sales, refunds, fees, ads and reserves inside it, running each platform through its own clearing account, tracking sales tax by who collected it, and booking cost of goods sold from inventory. ZeraBooks bookkeeping services keep those books monthly from your uploads.
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GROSS UP THE PAYOUT
Why is a Shopify or Amazon payout not your sales figure?
Shopify, Amazon, Etsy, Stripe and PayPal pay you what is left after they take their cut. If the books record only the deposit, sales are understated and every fee disappears. Here is one fictional two-week Amazon settlement for a kitchenware seller, March 1 to 14, 2026.
| Settlement line | Amount |
|---|---|
| Product sales | 24,860.00 |
| Shipping charged to customers | 1,240.00 |
| Sales tax collected from customers | 1,989.60 |
| Marketplace facilitator tax kept by Amazon | (1,989.60) |
| Refunds to customers | (1,318.00) |
| Referral (selling) fees | (3,729.00) |
| Fulfillment fees | (4,212.75) |
| Sponsored ads billed to the account | (1,456.30) |
| Reserve held this period | (2,150.00) |
| Reserve from last period released | 1,820.00 |
| Deposited to the bank | 15,053.95 |
The bank shows one deposit of $15,053.95. The business actually sold $26,100.00 including shipping, gave back $1,318.00 and paid $9,398.05 in fees and ads. The sales tax line comes in and goes straight back out, because Amazon collects and pays it to the states. The reserve is still your money, held for possible claims, so it belongs on the balance sheet, not in expenses.
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THE JOURNAL ENTRY
What journal entry records a marketplace payout?
One entry per settlement puts every line where it belongs. The other side of the net deposit is a clearing account for that platform, not the bank.
| Account | Debit | Credit |
|---|---|---|
| Amazon clearing | 15,053.95 | |
| Amazon reserve held (2,150.00 held less 1,820.00 released) | 330.00 | |
| Sales returns and refunds | 1,318.00 | |
| Marketplace selling fees | 3,729.00 | |
| Fulfillment fees | 4,212.75 | |
| Advertising | 1,456.30 | |
| Product sales: Amazon | 24,860.00 | |
| Shipping income | 1,240.00 | |
| Totals | 26,100.00 | 26,100.00 |
When the $15,053.95 lands in the bank, that line is categorized to Amazon clearing, and the clearing account goes back to 0.00. Any balance left in a clearing account at month end means a payout and a deposit don’t match yet: a deposit still in transit, or a settlement nobody booked. The tax collected and withheld nets to zero, so it is left out of this entry and kept in the settlement file.
ONE CLEARING ACCOUNT PER PLATFORM
Do you need a separate account for each sales channel?
Yes. Each platform pays on its own schedule, takes its own fees and holds its own reserves. Keeping one clearing account for each lets you prove each one to zero every month.
Shopify Payments
Card processing fees are taken out before the payout, so the deposit is net again. Gross up from the payout report: orders, refunds, processing fees, any chargeback and its fee.
Amazon
Settlements run about every two weeks and rarely line up with month end. Book each settlement by its own dates, and the month-end clearing balance is the part of a settlement that hasn’t been paid out yet.
Etsy
Gross up from Etsy’s monthly statement, which lists the sales, refunds and each fee. Book it the same way, through an Etsy clearing account.
Stripe and PayPal
Each fee is shown against each payment. A PayPal balance you spend from directly works like a bank account, so it gets its own statement each month, not just the transfers out.
Your own revenue lines
Product sales by channel (Shopify, Amazon, Etsy, wholesale) as sub-accounts of revenue, plus shipping income. One refunds account for all channels is usually enough.
SALES TAX
Who collects sales tax on online sales, the marketplace or you?
On a marketplace, usually the marketplace. Every state with a statewide sales tax, plus Washington DC, now has a marketplace facilitator law that makes platforms like Amazon and Etsy collect and pay the tax on the sales they process. That is why the Amazon settlement above shows the tax coming in and going straight back out. For those sales, the books show no sales tax owed by you.
On your own site, the tax is yours. A Shopify store calculates tax at checkout, but the money comes to you in the payout and you register, file and pay it in each state where you have to collect. Most states set that point at $100,000 of sales into the state in a year, and a few are higher. Tax collected on your own site goes to a sales tax payable account, never to revenue, and is cleared when you file. Which states you must register in is a question for your sales tax adviser; the books show the sales by state that answer it.
INVENTORY AND COST OF GOODS SOLD
How do you work out cost of goods sold for an online store?
Stock you buy is inventory, an asset, until it sells. Cost of goods sold is what the stock that left the shelf cost you. The usual way to get it each month: start with what you had, add what you bought, subtract what is left on the count. Here is March for the same fictional seller, all channels.
| March 2026 | Amount |
|---|---|
| Beginning inventory, March 1 (last month’s count) | 38,400.00 |
| Add: stock purchased from suppliers | 21,750.00 |
| Add: inbound freight and duties on that stock | 1,180.00 |
| Goods available to sell | 61,330.00 |
| Less: ending inventory, March 31 (count at cost) | (40,215.00) |
| Cost of goods sold | 21,115.00 |
| Net sales, all channels | 52,300.00 |
| Gross profit (59.6% margin) | 31,185.00 |
Purchases are booked to inventory when they are paid, and one month-end journal entry moves $21,115.00 from inventory to cost of goods sold. Freight to get stock to you is part of its cost; shipping orders out to customers is a selling expense. If the margin jumps around from month to month while prices stay put, the count is usually the problem, not the sales.
RETURNS, CHARGEBACKS AND 1099-K
How do you record returns, chargebacks and Form 1099-K?
Returns
The refund goes to sales returns and refunds, so gross sales stay visible on the profit and loss. If the item goes back on the shelf, it is back in the next count. If it is thrown away, it is part of cost of goods sold through the lower count.
Chargebacks
When a customer disputes a card charge, the processor takes the money back out of your payout, often with a fee. Book the amount against sales returns or a chargeback losses account and the fee to merchant fees. If you win the dispute, the money comes back in a later payout and the entry reverses.
Form 1099-K
A platform files a 1099-K for you only when your gross payments through it top $20,000 and your transactions top 200 in the year, under the threshold the One, Big, Beautiful Bill restored. The form shows gross sales before refunds and fees, so it will never match your deposits. Grossed-up books match it, line for line by platform. All of the income is taxable whether a form arrives or not.
Reserves
A balance held by a marketplace is an asset until it is released. A reserve that only grows is worth a call to the platform before it becomes a cash problem.
IN ZERABOOKS
How does ZeraBooks keep an online store’s books?
ZeraBooks doesn’t connect to Shopify, Amazon or any other platform, and has no bank feed. You send us the files; we do the rest.
- 1
You upload the month
Bank and card statements, each platform’s payout or settlement reports, supplier invoices and your month-end inventory count, through your upload portal.
- 2
Each payout is grossed up
One journal entry per payout through that platform’s clearing account, split into sales, shipping, refunds, fees, ads and reserves like the example above.
- 3
Inventory and tax are booked
Cost of goods sold from your count, and sales tax from your own site held as a liability until you file.
- 4
Every account is proven
Each bank and card statement must tie to its printed balances, and each clearing account must be at zero or explained, before the month is signed off. You see the reports in a read-only login, on the schedule you choose.
Does ZeraBooks connect to Shopify or Amazon?
No. ZeraBooks has no platform connection and no bank feed. You upload your bank and card statements and each platform’s payout or settlement reports through your upload portal, and we book them from those files.
Should I record ecommerce sales at the gross or the net amount?
Gross. Record the full sale, then the refunds, fees and ads as their own lines. Net books understate revenue, hide what each platform costs you and won’t match your Form 1099-K.
Do I charge sales tax on Amazon and Etsy orders?
The marketplace does. Every state with a statewide sales tax, plus DC, requires marketplaces to collect on the sales they process. Your own site is different: there the tax is yours to register for, collect and file where you have to.
Is inventory an expense when I buy it?
For the books, no. It is an asset until it sells, and then it becomes cost of goods sold. Your tax preparer decides how inventory is treated on the return; the books still need the monthly count to show a real margin.
My store’s books are a year behind. Where do I start?
With every bank, card and platform statement since the last month you trust, plus the payout reports for the same months. Books that were kept on net deposits usually need a bookkeeping cleanup first. For a sense of what monthly help runs, see how much does a bookkeeper cost.
How much does ecommerce bookkeeping cost with ZeraBooks?
The service starts at $150 a month (USD), for sellers anywhere in the world, and is quoted after a free call based on platforms, order volume and how far behind the books are. If you would rather do it yourself, ZeraBooks AI bookkeeping is $79 a month billed annually.
WE DO YOUR BOOKS
Spend the time on products.
Hand over the payouts.
Running a kitchen or selling homes instead? See bookkeeping for restaurants or bookkeeping for real estate agents. Selling online? Tell us which platforms you use, how many orders a month and how far behind the books are, and we’ll quote the monthly work before anything starts. Book the free call
Last updated October 17, 2026 · Written by Damin Mutti, founder of ZeraBooks