Accounting for Shopify and Amazon Sellers
Amazon settlements and fees, FBA inventory, Shopify payouts and one profit and loss by channel.
Shopify and Amazon seller accounting
Shopify and Amazon seller accounting turns two very different payout systems into one set of books: Amazon settlement and transaction reports broken into sales, fees, refunds, reserves and marketplace tax; Shopify payouts traced back to orders; FBA inventory and reimbursements recorded at cost; and one profit and loss statement that shows what each channel really earns. Atidiv does this for US consumer brands in QuickBooks, Xero or NetSuite. It starts with a review of your current books, and it is priced hourly, as a monthly retainer, or as a project.
Two channels, two sets of rules
A brand selling on both has two businesses with two sets of rules. Shopify is your store: you set the price, collect the tax where you owe it, and pay processing fees. Amazon is a marketplace: it sets many of the fees, holds some of the money for a while, collects the sales tax, and pays you what is left every settlement period. Books that treat both the same way end up with the wrong margin for each.
What makes Shopify accounting different
On Shopify, the store is yours and so is the tax. Sales tax you collect is a liability until you pay it, never revenue. Each Shopify Payments payout is net of processing fees, refunds and disputes. The Shopify Payments activity report shows gross activity, fees and payouts for a date range. Shopify says it is not a revenue statement, and it leaves out Shopify billing fees and third-party payment methods, which we reconcile from their own records. App subscriptions, shipping labels and Shopify's own bill are booked as expenses. They are not netted against sales.
Selling on both? See what each channel really earns after fees.
What makes Amazon accounting different
Amazon offers two views of the same money. Settlement reports cover each payout cycle. Date Range reports cover activity within dates you choose, with a line for each order, refund, fee, transfer and adjustment. Amazon states plainly that the totals will not match, because settlement reports follow payout timing and Date Range reports follow activity timing. The Date Range transaction report carries separate columns for product sales, shipping credits, promotional rebates, selling fees, FBA fees, other transaction fees and marketplace withheld tax.
We use the transaction detail to book revenue and fees in the month they happened, and the settlement report to tie each payout to the bank. Where Amazon holds funds under a delivery-date reserve, those amounts are tracked as a receivable until they are released, rather than disappearing from the month.
- Referral fee: A percentage of the total price or a per-item minimum, whichever is greater; varies by category. Selling expense, by channel.
- FBA fulfillment fee: Picking, packing and shipping each order, plus customer service and returns, per Amazon’s FBA costs overview. Fulfillment cost, which many brands treat as part of COGS.
- Monthly storage and aged inventory: Space your stock takes in Amazon’s fulfillment network each month, plus a monthly charge on items stored for more than 181 days. Warehousing cost, watched for slow-moving stock.
- Inbound placement fee: Distributing your inventory to fulfillment centers close to customers. Inbound freight, part of landed cost.
- Returns processing fee: Orders where Amazon offers free return shipping. Returns cost, reported next to refunds.
- Removal and disposal fees: Returning or disposing of stock held at Amazon. Inventory write-off cost. Whether fulfillment fees sit in COGS or operating expenses is a policy you set with your accountant. We apply it the same way every month so margins stay comparable.
Stock at Amazon is still your inventory until it sells, so it belongs on your balance sheet at cost. We reconcile units at Amazon against your inventory system at each close, and record shrinkage, removals and disposals as they happen.
When Amazon loses or damages FBA stock, its FBA inventory reimbursement policy says it will replace the item or pay you for it. For losses before a customer orders, Amazon reimburses the sourcing cost, which sellers can enter themselves; if they do not, Amazon uses its own estimate. The policy caps reimbursement at $5,000 per unit. We book each reimbursement against the inventory it replaces, and your unit costs give you the numbers to check that Amazon’s estimate is right.
A refund on Amazon reverses the sale, appears in the transaction report with its own fee adjustments, and can bring a unit back into sellable or unsellable stock. We record each part separately, so refunds, fee credits and returned inventory show up where they belong, and return rates by product can be read from the books.
Amazon says all US states with a sales tax have marketplace facilitator laws as of January 1, 2023. On those sales Amazon calculates, collects and remits the tax, and shows it in your reports as marketplace withheld or marketplace facilitator tax. Sellers cannot opt out. Amazon is not responsible for your income or gross receipts taxes, and says you may still have a reporting obligation for the sales it collected on. We keep that tax out of your revenue and report Amazon sales by state for your adviser.
How it starts
Four steps from a review of your reports to a monthly close.
We look at your Seller Central and Shopify reports, your accounting file and your bank, and list what is missing or booked from deposits.
We agree a chart of accounts with revenue, each fee type and COGS by channel, and a policy for fulfillment fees and reserves.
We rebuild past months from the transaction reports so the history is usable.
Each month we reconcile, close and review the numbers with you.
One set of books across both
The end result is one close with revenue, fees, COGS and gross margin by channel, side by side. That is the view that answers the questions sellers actually ask: whether Amazon is profitable after fees and storage, whether FBA is worth it against fulfilling yourself, and what a product earns on each channel. This sits within our bookkeeping services, and our finance and accounting team can add forecasting, cash planning and CFO support.
How pricing works
Price depends on order volume, the number of channels and marketplaces, entities, and how much history needs rebuilding. Hourly support suits smaller sellers or seasonal help. A fixed monthly retainer covers ongoing bookkeeping and the close, based on volume, entities and complexity. A project covers a clean-up, a migration, a software set-up or a backlog. The proposal follows the review.
Frequently asked questions about Shopify and Amazon seller accounting
QuickBooks, Xero or NetSuite, in your own file.
Yes. We use the transaction detail for revenue and fees, and the settlement report to tie each payout to the bank.
Yes. We record each reimbursement against the inventory it replaces and keep your sourcing costs current, which is what Amazon uses to value pre-order losses.
Amazon collects and remits the tax on those sales. We keep it out of revenue and give your adviser Amazon and Shopify sales by state. Filing on your Shopify sales stays with your adviser.
Yes. The monthly close reports revenue, fees, COGS and gross margin for Amazon and Shopify separately and combined.
Yes. Each extra channel is reconciled from its own payout reports and added to the same chart of accounts.