Amazon to Xero Integration: Complete Setup Guide (2026)

Amazon is the world’s largest marketplace, and accounting for it is one of the hardest things an e-commerce merchant does. According to Jungle Scout’s 2024 Amazon Seller Report, 44% of Amazon sellers cite bookkeeping and accounting as one of their biggest pain points — more than logistics, advertising, or competition. The culprit is almost always the settlement report: a bi-weekly deposit that buries 15 or more fee types inside a single net figure.

This guide shows you how to connect Amazon to Xero correctly using SyncTools. You’ll learn what gets synced, how to map fees to the right Xero accounts, and how the reconciliation logic eliminates manual journal entries entirely.

For broader context on using Xero for e-commerce, see the Xero eCommerce accounting guide.

TL;DR: 44% of Amazon sellers name bookkeeping as their #1 pain point (Jungle Scout, 2024). The fix is a direct Amazon-to-Xero integration that maps gross sales, FBA fees, referral fees, and settlements to separate accounts automatically. SyncTools handles the full setup in under 15 minutes — no manual journal entries required.

Why Is Amazon Accounting So Hard in Xero?

Amazon’s settlement structure is designed for paying sellers, not for informing their accountants. The bi-weekly deposit is a net figure that has already subtracted FBA fulfillment fees, referral fees, storage fees, advertising charges, customer refunds, and any subscription costs. Jungle Scout (2024) found that 44% of sellers struggle with this — and most of them are booking the net deposit as revenue, which understates gross sales and makes fees invisible on the P&L.

An e-commerce seller reviewing Amazon order data and financial reports on a laptop at their desk

Here’s what makes Amazon specifically difficult compared to other channels:

Settlement timing is unpredictable. Amazon holds funds for approximately 14 days and releases them on a bi-weekly cycle. The deposit date rarely aligns with the original sale dates, so a cash-basis approach will always misstate revenue by period.

The settlement report is dense. A single settlement file can contain hundreds of line items across multiple transaction types — product charges, shipping credits, fee adjustments, reimbursements, promotional rebates, and more. Manual processing is error-prone and time-consuming.

FBA fees are embedded, not separated. Amazon doesn’t send a separate invoice for FBA costs. Fulfillment fees, storage fees, and removal fees are deducted inside the settlement. Unless you extract them explicitly, you can’t see what FBA actually costs per unit.

Multi-currency adds another layer. Sellers on Amazon UK, EU, or CA marketplaces receive deposits in different currencies. Without a proper integration, exchange rate handling in Xero requires manual intervention on every settlement cycle.

So what’s the answer? Automate the extraction. A purpose-built integration reads every settlement line and maps it to the correct Xero account — gross sales to revenue, fees to expense, refunds to contra-revenue — before the deposit ever hits your bank feed.

For a solid foundation on Amazon bookkeeping, the Amazon seller accounting guide covers the full financial picture.

Citation capsule: According to Jungle Scout’s 2024 Amazon Seller Report, 44% of Amazon sellers identify bookkeeping and accounting as one of their primary business pain points — a higher rate than logistics or advertising challenges. The root cause is Amazon’s net settlement structure, which bundles 15+ fee types into a single bi-weekly deposit.

What Does SyncTools Sync from Amazon to Xero?

SyncTools syncs every transaction type that appears in an Amazon settlement report — not just the top-line sales figure. With approximately 1.9 million active third-party sellers on Amazon worldwide (Red Stag Fulfillment, 2025), most are running some version of Amazon bookkeeping. Very few are breaking down all the fee types correctly.

Here’s every transaction type SyncTools maps to Xero:

Amazon Transaction Type	Xero Destination
Gross product sales	Amazon Sales (revenue account)
Customer refunds	Sales Returns (contra-revenue)
FBA fulfillment fees	FBA Fulfillment Fees (expense)
Referral fees	Amazon Referral Fees (expense)
FBA storage fees	FBA Storage Fees (expense)
FBA removal / disposal fees	FBA Removal Fees (expense)
Amazon advertising charges	Amazon Advertising (expense)
Subscription fees (Pro seller)	Subscription Fees (expense)
Reimbursements (lost/damaged)	Other Income or COGS offset
Multi-currency sales	Original currency, Xero handles FX
Net settlement deposit	Bank reconciliation via Amazon clearing account

Why does the clearing account matter? Without it, you’d have to manually match the net bank deposit to the individual transactions in Xero. SyncTools posts gross sales and fees to their respective accounts as they occur, then maintains an Amazon clearing account that absorbs the net difference. When the deposit arrives in your Xero bank feed, it reconciles against the clearing balance in a single click.

Our finding: When Amazon fees are properly mapped in Xero, sellers consistently discover their true per-channel margin for the first time. FBA costs that were invisible inside a net-deposit workflow often represent 25–40% of gross sales. A channel that looked profitable on a cash-basis view sometimes delivers a 3–6% net margin once fees are properly surfaced in the P&L.

For a deeper breakdown of every FBA fee type, see the Amazon FBA fee reconciliation guide.

Citation capsule: Third-party sellers accounted for 61% of paid units sold on Amazon in Q4 2025 (Marketplace Pulse), representing a marketplace of approximately 1.9 million active sellers worldwide (Red Stag Fulfillment, 2025). The vast majority process bi-weekly settlement reports that combine 15+ transaction types into a single net deposit — creating a bookkeeping challenge that manual entry cannot reliably solve.

How to Connect Amazon to Xero: Step-by-Step Setup Guide

Setting up the Amazon Xero integration in SyncTools takes five steps. Most sellers complete the full process — authentication, account mapping, and first sync — in under 15 minutes.

Step 1: Connect Amazon Seller Central to SyncTools

Log in to your SyncTools account and click Add Integration from the dashboard. Select Amazon Seller Central from the integration list. SyncTools will redirect you to Amazon’s OAuth authorization page — this is Amazon’s standard secure flow, and SyncTools never stores your Amazon credentials.

Grant the required read permissions for orders, settlement reports, and fees. If you operate multiple Amazon marketplaces (US, UK, EU, CA), you can connect each marketplace as a separate integration or link them under a unified account.

Step 2: Connect Xero to SyncTools

From the SyncTools integrations dashboard, click Add Accounting System and select Xero. Authenticate via Xero’s OAuth flow — no API keys or manual configuration required. Select the Xero organisation you want to sync to. If you manage multiple Xero organisations, select the correct one for this Amazon account.

SyncTools will read your existing Xero chart of accounts in the next step, so it’s worth having Xero open in a separate tab as you work through the mapping.

Step 3: Map Your Xero Chart of Accounts

This is the most important step. SyncTools presents a mapping screen with each Amazon transaction type on the left and a Xero account selector on the right. For each type, choose the Xero account where you want those transactions to post.

Use the recommended chart of accounts in the next section of this guide as your starting point. If you haven’t yet created dedicated accounts for Amazon fees in Xero, pause here and add them — it takes five minutes and prevents reclassification work later.

Step 4: Configure Sync Preferences

SyncTools offers two sync modes. Choose the one that fits your bookkeeping workflow:

Real-time sync — transactions post to Xero within minutes of the Amazon event. Best for high-volume sellers who want current data in Xero at all times.
Daily batch sync — a single summarized journal entry posts to Xero each night. Cleaner for sellers who review books weekly and don’t need intraday data.

You can also configure payout grouping (whether to group transactions by settlement period or by calendar day) and set your default currency for each marketplace.

Step 5: Run Your First Sync and Verify in Xero

Click Run First Sync to import historical transactions. SyncTools will pull the most recent settlement period by default — you can extend the lookback window in settings.

Open Xero and confirm that:

Product sales are posting to your Amazon Sales revenue account
FBA fees are posting to your FBA Fulfillment Fees expense account
Referral fees are posting to your Amazon Referral Fees expense account
The Amazon clearing account balance reflects your upcoming settlement amount
Any refunds appear as credit notes against the original revenue

Start your free SyncTools trial — connect Amazon to Xero in under 15 minutes at synctools.ai.

Xero Account Mapping: Recommended Chart of Accounts for Amazon Sellers

Getting the chart of accounts right before your first sync prevents months of reclassification. Xero reached 4.41 million subscribers as of FY25 (Xero FY25 Annual Results), and a large share are Amazon sellers who set up Xero with a generic template that misses the fee categories Amazon requires.

Financial reporting dashboard showing profit and loss accounts and expense categories in a clean accounting interface

Here’s the recommended account structure for Amazon sellers in Xero:

Income Accounts

Account Name	Account Type	What Goes Here
Amazon Sales	Revenue	Gross product sales from Amazon (before any deductions)
Amazon Shipping Income	Revenue	Shipping charges collected from Amazon customers
Amazon Reimbursements	Other Income	Compensation for lost or damaged FBA inventory

Cost of Goods Sold

Account Name	Account Type	What Goes Here
Amazon Referral Fees	Direct Costs	Per-sale commission (8–15% of sale price)
FBA Fulfillment Fees	Direct Costs	Per-unit pick, pack, and ship fees
Amazon Returns	Direct Costs	Cost of goods returned by customers

Operating Expenses

Account Name	Account Type	What Goes Here
FBA Storage Fees	Overhead	Monthly and long-term storage charges
FBA Removal Fees	Overhead	Removal or disposal order fees
Amazon Advertising	Advertising	Sponsored Products, Sponsored Brands, DSP
Amazon Subscription Fee	Overhead	Pro Seller monthly subscription

Current Assets / Liabilities

Account Name	Account Type	What Goes Here
Amazon Clearing Account	Current Asset	Temporary account — holds balance between sales and settlement payout
Sales Tax Payable	Current Liability	Amazon-collected sales tax (US marketplace facilitator rules apply)
Amazon Refunds Payable	Current Liability	Refunds initiated but not yet settled

Our finding: Placing FBA Fulfillment Fees and Referral Fees in COGS (rather than operating expenses) gives you a more accurate gross margin figure for Amazon as a channel. These fees are directly tied to each unit sold — they’re more like the cost of selling the product than overhead. Sellers who categorize them as COGS get a cleaner gross margin line that’s comparable to what a wholesale or retail channel would show.

For a broader view of how to structure your chart of accounts across multiple channels, see the eCommerce bookkeeping guide.

How to Handle FBA Fees, Storage Fees, and Referral Fees in Xero

The single most common Amazon bookkeeping mistake is treating FBA and referral fees as a single undifferentiated cost. With 82% of active Amazon marketplace sellers using FBA (Red Stag Fulfillment, 2025), and FBA fee totals routinely reaching 30–40% of gross revenue, getting this categorization right is critical for accurate margin reporting.

Source: Red Stag Fulfillment, 2025. Among active Amazon marketplace sellers.

Here’s how each fee type should be treated in Xero — and why the COGS vs. operating expense distinction matters:

FBA Fulfillment Fees are charged per unit shipped. They’re a direct cost of making a sale — closer to cost of goods sold than overhead. Map them to a COGS account under Direct Costs so they reduce your gross margin, not just your operating income. This gives you a per-channel gross margin figure that reflects the true cost of selling on Amazon.

Referral Fees work the same way. Amazon charges 8–15% of the sale price as a commission on every transaction. That’s a direct cost per unit sold. Treat it as COGS.

Storage Fees are different. Monthly storage and long-term storage fees accrue regardless of whether you sell anything in a given period. They’re period costs, not unit costs. Map them to operating expenses.

Advertising Fees (Sponsored Products, Sponsored Brands) are also period costs — you incur them to generate future sales, not in direct proportion to each unit. Map to an Advertising or Marketing expense account under operating expenses.

Why does this split matter? Because it gives you two meaningful numbers: gross margin (what you earn after the direct cost of each sale) and operating margin (what’s left after overhead and advertising). Sellers who lump all Amazon fees into a single “Amazon Fees” expense account lose visibility into both.

See the complete Amazon FBA fee reconciliation guide for a full breakdown of every fee category and the correct Xero account for each.

Citation capsule: 82% of active Amazon marketplace sellers use Fulfillment by Amazon (FBA), according to Red Stag Fulfillment (June 2025). FBA fees — including fulfillment, storage, and removal charges — routinely represent 30–40% of gross sales revenue, yet most sellers cannot see these costs as discrete P&L line items because they are embedded in the net settlement deposit.

How Does Reconciling Amazon Settlements in Xero Work?

Amazon settlement reconciliation is the step that breaks most manual bookkeeping workflows. The bi-weekly deposit is a net figure that doesn’t match any single transaction in Xero — it’s the sum of hundreds of transactions from the previous two weeks. With 68% of businesses actively seeking accounting automation to reduce manual effort (IFOL via Dokka, 2025), the appetite for a cleaner reconciliation process is clear.

A bookkeeper reviewing a printed settlement report against an accounting system on a second screen at a tidy desk

Here’s how SyncTools handles it:

During the settlement period, SyncTools posts each Amazon transaction to Xero in real time (or daily, in batch mode). Product sales go to your Amazon Sales account. FBA fees go to their expense account. The net of all these transactions accumulates in the Amazon clearing account — a current asset account that holds the receivable balance Amazon owes you.

When the settlement deposit arrives in your Xero bank feed, its amount exactly matches the Amazon clearing account balance. You click Reconcile in Xero, match the bank entry to the clearing account, and you’re done. No manual journal entries. No spreadsheet cross-referencing.

What about discrepancies? If the deposit doesn’t match the clearing account balance, SyncTools flags the difference and identifies which transaction types have a gap. In practice, discrepancies usually come from Amazon fee adjustments posted late or from a currency conversion rounding difference on multi-currency accounts.

Does reconciliation ever require manual intervention? Occasionally — when Amazon issues a retroactive fee adjustment for a prior settlement period. SyncTools flags these automatically so you can decide whether to post them to the current period or back-date the entry.

If you also sell on Shopify, the Shopify to Xero integration guide covers the same reconciliation workflow for Shopify payouts.

Frequently Asked Questions

Does SyncTools support Amazon to Xero integration?

Yes. SyncTools connects Amazon Seller Central to Xero and automates the sync of product sales, FBA fulfillment fees, referral fees, storage fees, advertising charges, refunds, and settlement payouts. Both FBA and FBM sellers are supported. Multi-currency accounts — including Amazon UK, EU, CA, and AU marketplaces — are handled natively through Xero’s built-in multi-currency features.

How does SyncTools handle Amazon settlement reports in Xero?

SyncTools reads every line of the Amazon settlement file and maps each component — gross sales, fee types, refunds, reimbursements — to a dedicated Xero account. When the net settlement deposit arrives in your Xero bank feed, it reconciles in one click against the Amazon clearing account SyncTools maintains. No manual journal entries are required. See the Xero eCommerce accounting guide for broader context.

What Amazon transaction types does SyncTools sync to Xero?

SyncTools syncs product sales revenue, customer refunds, FBA fulfillment fees, referral fees, storage fees, advertising charges, subscription fees, reimbursements for lost or damaged inventory, and the bi-weekly settlement payout. Each transaction type maps to a separate Xero account. Third-party sellers accounted for 61% of paid units on Amazon in Q4 2025 (Marketplace Pulse) — most have all of these transaction types in every settlement.

Can SyncTools handle Amazon multi-currency sales in Xero?

Yes. SyncTools supports multi-currency Amazon accounts and posts transactions in their original sale currency. Xero’s Established plan handles foreign currency invoicing, live exchange rate capture, and automatic gain/loss accounting. US, UK, EU, CA, and AU Amazon marketplaces are all supported. No manual currency conversion is required on your end.

How long does the Amazon Xero integration setup take?

Most sellers complete the full setup — connecting Amazon Seller Central, connecting Xero, mapping accounts, and running the first sync — in under 15 minutes. Authentication steps take under two minutes each via OAuth. Account mapping is the most time-intensive step, typically five to ten minutes, and it’s a one-time task. The Amazon seller accounting guide covers account structure in depth.

Does SyncTools support Amazon FBA and FBM sellers?

Yes. SyncTools supports both Fulfillment by Amazon (FBA) and Fulfillment by Merchant (FBM) sellers. FBA sellers get granular fee breakdowns including fulfillment, storage, and removal fees. FBM sellers get order revenue and referral fee mapping without FBA-specific fee lines. With 82% of active Amazon sellers using FBA (Red Stag Fulfillment, 2025), the FBA fee mapping covers the vast majority of use cases.

How does SyncTools reconcile FBA fees in Xero?

SyncTools extracts FBA fulfillment fees, storage fees, and removal fees from each Amazon settlement report and maps them to dedicated Xero expense accounts. This makes FBA costs visible as discrete P&L line items rather than absorbed into a net deposit. Sellers can then see actual per-unit FBA costs, compare fulfillment cost trends across settlement periods, and evaluate whether FBA fee changes are affecting margin. The Amazon FBA fee reconciliation guide has the full fee schedule and journal entry walkthroughs.

Connecting Amazon to Xero Is Worth Doing Once, Correctly

Amazon accounting isn’t difficult once the integration is set up properly. The problem is that most sellers either import raw settlement deposits as revenue — which is wrong — or spend hours every two weeks manually extracting fee lines from settlement reports. Neither approach scales.

A direct Amazon Xero integration via SyncTools replaces both of those workflows. Gross sales post to Xero on the order date. Fees map to dedicated expense accounts automatically. The settlement deposit reconciles in one click when it hits your bank feed. And the first time you see your Amazon channel margin as a real P&L line — not just a net deposit in your bank — you’ll understand why the setup matters.