what accounting software do amazon sellers use

The short answer: QuickBooks or Xero, connected to Amazon through a sync tool

The overwhelming majority of Amazon sellers, from side-hustle FBA accounts to seven-figure private label brands, land on the same basic combination: a general ledger platform (QuickBooks Online or Xero) plus a connector app that translates Amazon's settlement data into entries the ledger can actually use. A smaller group of brand-new or very low-volume sellers get by on spreadsheets for a while. A handful of larger operations eventually move to NetSuite or another ERP once they outgrow small-business accounting software entirely, but that's not the norm for most sellers reading this.

The reason almost nobody uses QuickBooks or Xero straight out of the box for Amazon is simple: Amazon doesn't hand you a clean list of sales. It hands you a settlement report every one or two weeks that bundles gross sales, refunds, FBA fees, referral fees, storage fees, advertising spend, and reserve movements into one lump deposit. Import that deposit into your bank feed and categorize the whole thing as 'Amazon income,' and you've just erased the detail your tax return, your margin analysis, and any FBA reimbursement claim all depend on.

Why regular bookkeeping software can't read Amazon data on its own

QuickBooks and Xero were built around a world of invoices, direct customer payments, and bank deposits that match one transaction to one sale. Amazon's marketplace model doesn't work that way. A single settlement deposit can represent thousands of individual orders, dozens of fee types, tax collected and remitted by Amazon itself, and inventory reimbursements from lost or damaged FBA stock, all netted into one number that lands in your bank account.

This isn't a small niche problem. Third-party sellers now account for more than half of the physical goods sold on Amazon, according to Amazon's own investor disclosures, which means the majority of transaction volume flowing through the platform is exactly this kind of bundled, multi-line settlement data that standard accounting software has no built-in way to parse. Without a translation layer, you're either spending hours manually breaking down CSV exports every settlement period, or you're booking numbers that look fine on the surface but are wrong underneath.

The two-layer stack most sellers end up with

Once sellers hit even modest volume, the stack that works looks the same across most businesses: a ledger for the books, and a connector that sits between Amazon and the ledger. The connector pulls settlement data through Amazon's API, sorts it into revenue, refunds, fee categories, tax, and reserves, and posts a summarized journal entry for each settlement period instead of one messy deposit.

This is the layer that separates amazon accounting software from generic ecommerce accounting. Tools in this category include A2X, Link My Books, and BeanHawk, and while they differ on price and detail level, they all solve the same core problem: getting settlement complexity out of your bank feed and into structured, auditable entries.

• •Pulls raw settlement and transaction data directly from Amazon, not from a bank statement
• •Breaks fees into categories: referral, FBA fulfillment, storage, advertising, refund admin
• •Handles multi-currency settlements for sellers on Amazon.com, Amazon.ca, and Amazon.co.uk
• •Flags reimbursements and reserve changes separately from ordinary sales
• •Posts one clean journal entry per settlement period instead of dozens of line items

QuickBooks for Amazon sellers: what it does well and where it struggles

QuickBooks Online is the default choice for a lot of sellers, mostly because it's the software their CPA or bookkeeper already knows. Its bank feed rules, reporting suite, and integrations with tax prep tools are strong, and if you ever sell the business or need financials for a loan, buyers and lenders are used to seeing QuickBooks files.

Where quickbooks for amazon sellers falls short is the same place it falls short for any marketplace business: it has no native concept of an Amazon settlement, an FBA fee type, or a reimbursement. Left alone, it'll happily categorize your entire Amazon payout as one revenue line unless you build the detail in some other way. QuickBooks Self-Employed in particular is not built for this at all; it's designed for freelancers with simple, one-line transactions, and it breaks down fast once you're dealing with inventory and multi-line settlements.

Xero for Amazon sellers: the alternative worth knowing

Xero for amazon sellers is the second common path, especially for sellers based outside the US or selling across multiple Amazon marketplaces. Xero's multi-currency handling is generally considered cleaner than QuickBooks Online's, and its interface tends to be a bit more intuitive for people without a bookkeeping background.

The trade-off is availability of support. Fewer US-based bookkeepers and CPAs specialize in Xero compared to QuickBooks, so if you want a professional to eventually take your books off your hands, QuickBooks may be the easier long-term fit. Neither platform, again, understands Amazon settlement data natively. You still need a connector in front of either one.

A worked example: turning one Amazon settlement into real books

Say a hypothetical seller, Maple Ridge Goods, sells kitchen tools on Amazon and gets a two-week settlement deposit of $8,220. If you booked that deposit as revenue, your books would show $8,220 in sales and nothing else, which is wrong on every level. Here's what the settlement actually contained, in round hypothetical numbers:

Gross product sales of $18,400, minus customer refunds of $1,120, minus FBA fulfillment fees of $3,850, minus Amazon referral fees of $2,760, minus storage fees of $310, minus PPC advertising spend of $1,640, minus a $500 reserve held back by Amazon for the next period. Net that out and you get the $8,220 deposit that actually hit the bank account.

A connector tool takes that same settlement and posts it as separate lines: revenue, refunds, referral fees, fulfillment fees, storage fees, advertising, and a reserve receivable, all tagged to the correct dates. On top of that, a proper set of books also records cost of goods sold separately, matched to the units actually sold in that period, not the cash spent on inventory that month. Skip that step and your gross margin numbers will be meaningless, because purchasing and selling rarely happen in the same window.

Common mistakes sellers make with their books

Most of the mistakes that show up in Amazon seller books trace back to the same root cause: treating the bank deposit as the source of truth instead of the settlement report.

The fixes are usually simple once you know to look for them, but they add up fast if ignored for a full year.

• •Booking the net deposit as total revenue, which understates sales and overstates margin
• •Ignoring FBA reimbursements as if they weren't income; since 2025 Amazon reimburses lost or damaged inventory based on the seller's actual manufacturing or sourcing cost when provided (see Amazon's FBA reimbursement policy), and those payouts need to be recorded, not lumped into general sales
• •Recording inventory purchases as an expense the moment you pay for them instead of capitalizing them and expensing as COGS when sold
• •Mixing cash and accrual methods depending on which report was open at the time
• •Recording sales tax that Amazon collects and remits on your behalf as if it were your own revenue, when it's actually a liability passing through your books
• •Reconciling to the bank statement date instead of the settlement period, which throws off month-end closes

Sales tax, 1099-Ks, and why the software choice matters here too

Sales tax used to be one of the messiest parts of Amazon accounting, and it still trips people up, but the mechanics have shifted. Following the Supreme Court's 2018 ruling in South Dakota v. Wayfair, states gained the ability to require out-of-state sellers to collect tax based on economic nexus, meaning sales or transaction volume, not just a physical office or warehouse in the state. On top of that, nearly every state with a sales tax has since adopted marketplace facilitator laws requiring platforms like Amazon to collect and remit sales tax on third-party sales directly, as tracked by the Sales Tax Institute.

That doesn't mean sales tax is fully off your plate. You may still owe registration and filing obligations in states where you have nexus through non-marketplace sales, and your software needs to correctly separate 'tax Amazon collected for me' from 'tax I need to handle myself.' Getting that distinction wrong in your ledger is a common source of overstated liabilities and confused filings.

1099-Ks add another layer worth watching. The IRS reporting threshold for third-party platforms has been changing rather than staying fixed at the old $20,000 and 200-transaction level, according to the IRS's own guidance. More sellers are receiving 1099-Ks each year as thresholds phase down, and if your books don't already reconcile to Amazon's own settlement totals, that form can create a mismatch that draws unwanted attention at tax time.

How to choose and what to do next

If you sell only on Amazon, the choice mostly comes down to whether you or your bookkeeper prefer QuickBooks or Xero, since either works fine once paired with a proper connector. If you also sell on eBay or run a Shopify store, look for a connector that covers your whole channel mix rather than picking separate ebay accounting software and shopify accounting software tools that don't talk to each other; consolidating everything into one ledger makes tax time and profitability analysis far less painful. Sellers running multiple channels through one system, sometimes called connecting amazon, shopify, or ebay to quickbooks, save real hours every month compared to reconciling each channel by hand.

The practical next steps are straightforward: pick a ledger (QuickBooks or Xero), pick a connector built specifically for Amazon settlement data rather than a generic bank import, and set a habit of closing your books monthly against Amazon's settlement reports, not your bank statement. If you want a purpose-built option that syncs directly into either ledger and handles FBA reimbursements as part of the same feed, Amazon accounting software that syncs to QuickBooks & Xero is worth a look before you build a manual process you'll just have to unwind later.

None of this requires perfection on day one. It requires picking a system that treats settlement data as the real transaction record, and staying disciplined about not letting the bank deposit stand in for it.