---
title: "Ecommerce bookkeeping services | Ledgerbrook"
source: https://ledgerbrook.com/industries/ecommerce/
description: "Ecommerce bookkeeping in QuickBooks Online: a clearing account per channel, fees, inventory, COGS and marketplace sales tax."
---

[Industries](/industries/)

# Ecommerce bookkeeping services

## What does ecommerce bookkeeping include?

Ecommerce bookkeeping records each sales channel's gross sales, fees, refunds and payouts through a clearing account, tracks inventory and cost of goods sold by product, and separates sales tax the store collected from tax a marketplace collected for it. Every channel's payouts tie to the bank, and the books close by the 5th business day.

Common for ecommerce stores

- Shopify, Amazon and Etsy payouts were all booked straight to Sales, so revenue is the net of fees and nobody knows what the fees were
- The 1099-K from Etsy says $58,000 and the books show $49,000 in sales for the same year
- Inventory has sat at the same balance since the opening entry, and every purchase of stock went to Cost of Goods Sold
- Sales Tax Payable has a balance nobody can explain, because tax Amazon collected and remitted was booked as if the store owed it
- Stock in an FBA warehouse and at a 3PL was never counted, so the year-end inventory figure is a guess

In detail

## Why a payout is not a sale

Ecommerce bookkeeping starts from the fact that no sales channel pays you what your customers paid. Shopify, Amazon, Etsy and eBay each collect the money, take their fees, hold back refunds and reserves, and send what is left in a lump that covers dozens or hundreds of orders. Book the deposit as Sales and the books understate revenue by every fee, hide every refund, and leave nothing to check the 1099-K against.

The fix is the same for every channel: record gross sales and each deduction from the channel’s own report, and let the deposit clear a holding account. This page covers what that looks like for a store selling on several channels at once, plus the two things a payment app never has to deal with: inventory and marketplace sales tax. The method for a single processor such as Square or Stripe, with one payout worked line by line, is in [payment apps in QuickBooks](/blog/payment-apps-in-quickbooks-online/). Each marketplace has its own page: [Shopify](/blog/shopify-and-quickbooks-online/), [Etsy](/blog/etsy-bookkeeping/) and [Amazon](/blog/amazon-seller-bookkeeping/), and which platforms collect sales tax for you is in [does Etsy, eBay or Shopify collect sales tax?](/blog/marketplace-sales-tax/)

## One clearing account per sales channel

A clearing account is an Other Current Assets account that stands in for the channel. Sales go in at gross, fees and refunds come out, and each payout moves the rest to the bank. Give every channel its own (`Shopify Clearing`, `Amazon Clearing`, `Etsy Clearing`, `eBay Clearing`) so each balance can be checked against that channel’s report on the last day of the month. A shared account hides which channel is wrong.

The channels differ in when they pay, what they deduct and who collects sales tax. These are the published US terms, read October 24, 2026; new accounts and accounts under review can be held longer.

| Channel | When payouts arrive | What comes out before the payout | Who collects sales tax |
| --- | --- | --- | --- |
| Shopify Payments | Minimum settlement time of 3 business days; Friday to Sunday payments go out as one payout ([Shopify](https://help.shopify.com/en/manual/payments/shopify-payments/supported-countries/united-states/payouts)) | Processing fees, refunds, chargebacks, reserves | You, except on Shop app orders. Shopify “doesn’t remit or file your taxes for you” ([Shopify](https://help.shopify.com/en/manual/taxes/us)), and its automated filing is closed to new stores and ends with sales through December 31, 2026 |
| Amazon | On a settlement cycle, commonly every 14 days; the exact dates are in the Seller Central Payments dashboard | Referral fees by category, the $39.99 monthly Professional plan or $0.99 per item, FBA fees, refunds, reserves ([Amazon](https://sell.amazon.com/pricing)) | Amazon, as marketplace facilitator |
| Etsy | Daily, weekly, every two weeks or monthly, as the seller chooses ([Etsy Payments policy](https://www.etsy.com/legal/etsy-payments/)) | $0.20 per listing, a 6.5% transaction fee, 3% plus 25 cents processing, Etsy Ads and Offsite Ads ([Etsy fees](https://www.etsy.com/legal/fees/)) | Etsy, as marketplace facilitator |
| eBay | On demand by default, or automatic daily, weekly, every two weeks or monthly; proceeds typically become available 1 to 2 days after the buyer’s payment is confirmed ([eBay](https://www.ebay.com/help/selling/getting-paid/getting-paid-items-youve-sold?id=4814)) | Insertion fees, final value fees, promoted listing fees, refunds | eBay, as marketplace facilitator |
| PayPal | Stays in the PayPal balance until transferred | Fees and refunds, from the balance | You, for sales on your own site |

Two rows need more than the table gives them. PayPal holds a balance that can pay bills and sit for weeks, so set it up as its own Bank account and reconcile it, rather than as a clearing account that should empty itself. And an eBay balance left on demand behaves the same way until it is withdrawn: the clearing account carries it, and the month-end check is that balance against eBay’s.

## A month on one channel, worked

An Etsy shop sells 80 orders in October: $4,000.00 of items and $400.00 of shipping charged to buyers. Etsy collects $300.00 of sales tax on those orders and remits it itself. The shop takes weekly deposits, and its September balance was paid out on September 29 with no sales on the 30th, so the month starts at zero.

| Etsy activity, October | Amount |
| --- | --- |
| Item sales | 4,000.00 |
| Shipping charged to buyers | 400.00 |
| Transaction fees, 6.5% of $4,400.00 | −286.00 |
| Payment processing, 3% of $4,700.00 plus 25 cents on 80 orders | −161.00 |
| Listing and renewal fees, 130 at $0.20 | −26.00 |
| Etsy Ads | −60.00 |
| **Left for deposit** | **3,867.00** |

Etsy charges processing on the order total including tax, which is why that fee is figured on $4,700.00 while the transaction fee, for a US seller, is not charged on sales tax. The tax itself never reaches the seller’s books: Etsy collects it and pays the state.

The month goes into QuickBooks Online as one journal entry from Etsy’s monthly statement, plus the four deposits, each coded to the clearing account from the bank feed:

| Date | Account | Debit | Credit |
| --- | --- | --- | --- |
| Oct 6 | Business Checking | 812.40 | |
| Oct 6 | Etsy Clearing | | 812.40 |
| Oct 13 | Business Checking | 905.10 | |
| Oct 13 | Etsy Clearing | | 905.10 |
| Oct 20 | Business Checking | 960.25 | |
| Oct 20 | Etsy Clearing | | 960.25 |
| Oct 27 | Business Checking | 882.25 | |
| Oct 27 | Etsy Clearing | | 882.25 |
| Oct 31 | Etsy Clearing | 4,400.00 | |
| Oct 31 | Sales | | 4,000.00 |
| Oct 31 | Shipping Income | | 400.00 |
| Oct 31 | Marketplace Fees | 312.00 | |
| Oct 31 | Merchant Service Fees | 161.00 | |
| Oct 31 | Advertising | 60.00 | |
| Oct 31 | Etsy Clearing | | 533.00 |

`Etsy Clearing` takes in $4,400.00 and gives out $533.00 of fees and $3,560.00 of deposits, leaving $307.00 on October 31. That is the month-end check: Etsy’s own balance for the shop on the same date should also be $307.00, made up of sales from the last days of the month that had not been deposited yet. When the two disagree, a deposit was coded to Sales instead of the clearing account, a refund or fee adjustment is missing, or a week was entered twice.

Recording sales at gross is also what makes the 1099-K tie. Etsy’s form reports gross sales including shipping, before fees, and leaves out the sales tax Etsy remits for you; how each platform builds its figure is in [why your 1099-K doesn’t match your books](/blog/1099-k-and-your-books/).

Amazon works the same way with more lines. A settlement report carries principal, shipping credits, promotional rebates, referral fees, FBA fulfillment fees, storage fees, refunds and reserve movements, and a reserve held back from one settlement and released in the next can make a settlement come out negative. Each line type gets its own account once, and every settlement follows the same mapping after that.

## Inventory and cost of goods sold

Stock bought for resale is an asset until it sells. Booked straight to Cost of Goods Sold, a big October purchase makes October look like a loss and November look unusually profitable, and gross margin by month means nothing.

There are two ways to keep it right:

- **Perpetual.** QuickBooks Online tracks quantity on hand and moves the cost of each unit to Cost of Goods Sold as it sells. Quantity tracking is in the Plus and Advanced plans, and both use FIFO. It needs every sale to reach QuickBooks as item-level detail, which usually means a connector, and it breaks when the channel’s product names and QuickBooks items drift apart.
- **Periodic.** Purchases go to Inventory, the stock is counted at the end of the period, and the difference becomes Cost of Goods Sold in one entry. A small store with one warehouse or a spare room, a few hundred SKUs and summary sales entries can count monthly or quarterly and get accurate margins with far less upkeep.

The periodic calculation, for the same October:

> **Cost of Goods Sold** = Beginning Inventory + Purchases − Ending Inventory

- Beginning inventory, October 1: $12,000.00
- Purchases in October: $3,500.00
- Ending inventory from the October 31 count: $13,100.00
- **Cost of Goods Sold for October: $2,400.00**

Against $4,000.00 of item sales, that is a 40% gross margin before fees. Stock held by Amazon under FBA or at a third-party warehouse is still the seller’s inventory and gets counted from that warehouse’s inventory report, not left out because nobody can walk the shelves. Freight to bring stock in is part of its cost; shipping orders out to customers is an expense.

How the entries look under each system, the count adjustment for shrinkage and the small business tax exception in IRC §471(c) are worked through in our [journal entry for inventory](/blog/journal-entry-for-inventory/).

## Sales tax: what you collect and what a marketplace collects

Since _South Dakota v. Wayfair_ (2018), a state can require an online seller with no presence there to collect its sales tax once the seller passes that state’s economic threshold. Every state with a statewide sales tax has also passed a marketplace facilitator law, which makes Amazon, Etsy, eBay and Walmart collect and remit the tax on sales made through them. Missouri was the last, with marketplace rules effective January 1, 2023 ([REDW](https://www.redw.com/missouri-enacts-economic-nexus-marketplace-facilitator-laws/)), and its Department of Revenue says a seller who sells there only through a marketplace does not have to “register, collect or remit vendor’s use tax” (quoted by [TaxJar](https://support.taxjar.com/article/1075-missouri-sales-tax-filing-update-marketplace-facilitator-laws)).

The books follow who collected:

- **Marketplace sales.** The marketplace collects and remits, so the tax is not the seller’s liability. Leave it out of Sales and out of `Sales Tax Payable`, as in the Etsy month above. Booking it in and then “paying” it creates a balance the seller never owes.
- **Your own storefront.** On a Shopify store or your own site, you are the seller and the tax you charge is yours to file. Credit it to `Sales Tax Payable` when the sale is recorded, and reduce that account only when you pay the state.

The common mess is a mixed store whose Shopify tax and Amazon tax were booked the same way. `Sales Tax Payable` should match the tax due on your own returns at month end, state by state; anything left over is usually marketplace tax that never belonged there.

## What ecommerce bookkeeping software do you need?

The pages that rank for this question are product lists. What any setup needs is shorter:

- **An accounting file with one clearing account per channel**, reconciled monthly. QuickBooks Online and Xero both do this, and most tax preparers can work in either.
- **A way to get each channel’s activity in at gross.** For a small store that is one journal entry per channel per month from the channel’s statement. Higher volume usually means a connector that posts each payout as a summary entry; A2X, Link My Books, Synder and Webgility are among the apps built for it. A connector that posts every order as its own sale is what floods a file with thousands of transactions.
- **Inventory records that match a count**, whether QuickBooks quantity tracking, an inventory app, or the periodic method above.
- **A sales tax record by state** for your own storefront, from Shopify Tax or a sales tax app.

The test of any setup is the month-end check: every clearing account equals the channel’s own balance, and the bank reconciles.

## Common questions about ecommerce bookkeeping

### What is ecommerce accounting?

Ecommerce accounting is bookkeeping plus the analysis on top of it: margin by product and channel, cash forecasting around inventory buys, and the tax return. Bookkeeping is the part this page covers, getting every channel’s sales, fees, refunds and stock movements into the books correctly each month. Without that layer, the analysis has nothing reliable to work from.

### Do ecommerce businesses need accrual accounting?

A small online store can usually keep its tax return on the cash method, but its management books need inventory recorded as an asset either way, or margins are meaningless. The cutoff for the cash method under IRC §448(c) is a gross receipts test that starts at $25 million in the statute and is indexed for inflation every year, so it is higher than the $25 million some guides quote. Which method a particular store files on is a question for its tax preparer.

### How much can I sell online without paying taxes?

All sales income is taxable whether or not a form is issued. The 1099-K threshold for payment apps and marketplaces, more than $20,000 and more than 200 transactions in the year, only decides whether the platform sends a form; it is covered in [why your 1099-K doesn’t match your books](/blog/1099-k-and-your-books/).

### How much does an online bookkeeper cost?

Market rates and what moves them are in [how much a bookkeeper costs](/blog/how-much-does-a-bookkeeper-cost/). Our own prices are below.

Brick-and-mortar shops with a register and the same stock problems are covered on the [retail stores](/industries/retail-stores/) page.

## How much does ecommerce bookkeeping cost?

A store whose payouts were booked as sales for a year usually needs every channel’s statements pulled, each month grossed up through a clearing account, and inventory rebuilt from purchase records and a count. That is a [cleanup](/quickbooks-cleanup/) engagement, scoped to the number of months affected.

$99per month of backlog20% off 6+ months

After that, a [monthly close](/monthly-bookkeeping/) books every channel at gross, ties each clearing account to the channel’s balance, records inventory and cost of goods sold, and reconciles every account by the 5th business day. That is $99 a month (up to 3 accounts, up to 200 transactions a month), and $199 past either limit. Store owners can read how an engagement starts on the [outsourced bookkeeping page](/for-business-owners/). Other trades are on the [industries page](/industries/), and full pricing is on the [pricing page](/pricing/).

Or [send your file for a free review](/contact/?from=industries%2Fecommerce), with a written answer within 48 hours.

Ledgerbrook

Behind on your QuickBooks books?

Cleanup or catch-up

$99 per month of backlog, 20% off 6+ months

Turnaround

5 business days for a typical year

Monthly close

From $99 a file a month

[Get a free file review](/contact/?from=industries%2Fecommerce)

Free, no card, no obligation. A written answer within about 48 hours.

[See every price](/pricing/)

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