E-commerce
Ecommerce Bookkeeping for Amazon and Shopify Sellers: What to Track and Why Payouts Never Match
Quick answer
Ecommerce payouts never match sales because they are net of fees, shipping, ads, refunds and reserves. Record gross sales, post fees to their own accounts, track COGS when product ships, and reconcile every payout to the bank.
Why the numbers rarely add up
If you sell on Amazon or Shopify, you have probably looked at a bank deposit and wondered how it relates to your sales. It almost never matches. That gap is the core problem of ecommerce bookkeeping.
This guide explains why the numbers differ, what you need to track, and how to keep your books clean enough to know your real profit.
Why payouts do not match sales
A marketplace or payment processor does not deposit your sales. It deposits sales minus a list of things:
- Marketplace or processing fees
- Fulfillment and shipping charges
- Advertising costs charged against your balance
- Refunds and returns
- Reserves or holds
- Sales tax collected (in some cases)
Deposit timing is different too. A sale in one month can be paid out in the next. If you book the deposit as revenue, your income is wrong, your fees disappear, and your profit looks bigger than it is.
The right way: record gross sales, then the fees
Each payout should be broken back into its parts:
- 1Gross sales go to revenue.
- 2Fees, shipping and ad costs go to their own expense accounts.
- 3Refunds reduce revenue.
- 4The net deposit is what is left, and it should match your bank.
Marketplaces provide settlement or payout reports for this purpose. A bookkeeper reconciles each report to the bank deposit, so every dollar is accounted for.
Track each sales channel separately
If you sell on Amazon, Shopify and maybe Walmart or Etsy, keep revenue by channel. Fees, return rates and margins differ a lot between them. Combined numbers hide which channel is working. Our ecommerce bookkeeping service reconciles every channel into one set of books.
Inventory and cost of goods sold (COGS)
For product sellers, inventory is usually your biggest asset, and COGS is usually your biggest cost. Two things to get right:
- Buying inventory is not an expense yet. It is an asset until it sells.
- Cost hits your books when the product ships. That is COGS. It should match what you sold, not what you ordered.
Your inventory method matters. Many sellers use FIFO (first in, first out), which assumes the oldest stock sells first. Include freight-in and other landed costs in your product cost, or your margins will look better than they are. Ask your CPA which method fits your tax situation.
Sales tax: do not guess
Sales tax rules for online sellers are complicated and vary by state. In most states, marketplaces like Amazon collect and remit sales tax on marketplace sales. Sales on your own Shopify store are different: you may be responsible for collecting and filing. Keep sales tax collected out of revenue, track it by state, and confirm your obligations with a tax professional. Our tax deadlines checklist helps you plan filing dates.
Other things that trip up sellers
- Amazon reserves and holds: money that is yours but not in your bank yet.
- Returns and chargebacks: they arrive later, sometimes in a different month.
- Ad spend: often charged separately from payouts. Track it as marketing, by channel.
- Mixed accounts: use one bank account and card for the business.
- Sample and damaged inventory: write it off properly.
- Foreign currency: if you sell abroad, conversion differences need a home in your books.
The monthly numbers worth watching
- Revenue by channel
- Gross margin after COGS
- Total fees as a percent of sales
- Ad spend against revenue
- Inventory on hand vs. what you expect
- Cash vs. profit (they are not the same thing in ecommerce)
If you only look at one report, make it the profit and loss with COGS broken out. For more on cash, read how to improve cash flow.
Software: QuickBooks Online or Xero
Most ecommerce sellers do best with QuickBooks Online or Xero, plus a connector that pulls marketplace data in as summaries. Pushing every single order into your books creates thousands of lines nobody reviews. Summaries by payout, reconciled to the bank, are easier to audit. If you are weighing options, see QuickBooks Online vs. Desktop.
When to hire a bookkeeper
- Your deposits do not tie to your sales and you stopped trying.
- You are not sure what your margin is on each product or channel.
- You sell in several states or on multiple platforms.
- You are behind on months of reconciliation. Catch-up work can rebuild them.
Next steps
Know your real profit by channel, not just your deposits.
Frequently asked questions
Why does my Amazon payout not match my sales?
Payouts are net of fees, fulfillment charges, ad costs, refunds and reserves, and they are paid on a different schedule than the sales.
How do I record Shopify sales in QuickBooks?
Record gross sales to revenue, fees to expense accounts, and reconcile the net payout to your bank deposit. Summaries by payout work better than one line per order.
What is COGS for an ecommerce business?
The cost of the products you sold in the period, including freight-in and landed costs. It is recorded when the product ships, not when you buy it.
Do I have to collect sales tax on Amazon sales?
In most states Amazon collects and remits it for marketplace sales. Sales on your own store can be different, so confirm your obligations with a tax professional.
Should I track each channel separately?
Yes. Fees and margins vary by channel, and combined numbers hide that.
What accounting software works best for sellers?
QuickBooks Online and Xero are both common. Mispar works in either.
How much does ecommerce bookkeeping cost?
Mispar's flat plans are Startup $229/month, Grow $429/month and Premium $629/month. See [[pricing|/pricing]].
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Written by
Moshe
Senior Account Manager, Mispar
Moshe is a Senior Account Manager at Mispar who works directly with small business owners and freelancers to keep their books clean, reconciled, and tax-ready every month.
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