Running an eCommerce business means juggling dozens of platforms, marketplaces, payment gateways, and shipping tools each with its own reports, rules, and reconciliation quirks. That’s where the right Xero eCommerce integrations come into play. Instead of manually exporting reports from Shopify, tallying Amazon fees, or figuring out PayPal deposits, integrations help you bring everything into Xero accurately and efficiently.

In this blog, we’ll cover the most trusted Xero eCommerce integrations, including A2X, Synder, and Link My Books. Whether you’re selling on Amazon, Etsy, Shopify, WooCommerce, or multiple marketplaces, these integrations help you gain better financial control while saving hours of manual bookkeeping.

Xero is a cloud accounting software designed for growing businesses. Its flexibility, real-time reporting, and user-friendly interface make it ideal for eCommerce sellers. But it’s the power of Xero eCommerce integrations that truly unlocks its potential.

With the right connections, Xero can automatically pull in your sales, fees, refunds, shipping costs, taxes, and payouts. You can stop chasing spreadsheets and start focusing on insights.

Instead of entering sales from Amazon or Shopify manually, integrations post summarised, clean entries directly to your Xero account, keeping your records accurate and audit-ready.

What Makes a Good Xero Integration for eCommerce?

Not all integrations are created equal. When evaluating Xero eCommerce integrations, consider:

  • Accuracy: Does the tool capture all sales, refunds, and fees?
  • Marketplace compatibility: Can it connect to all your sales channels (e.g. Amazon, Shopify, Etsy)?
  • VAT/GST support: Is it built for your tax jurisdiction?
  • Support and reliability: Is there expert help when needed?
  • Reconciliation: Does it make bank matching easier?

Let’s explore some of the top Xero eCommerce integrations that meet these standards and are trusted by thousands of online sellers.

1. A2X: Gold Standard for Amazon & Shopify

A2X is one of the most established Xero eCommerce integrations in the market, particularly known for handling Amazon and Shopify sales. It simplifies one of the trickiest parts of eCommerce accounting: reconciling payouts to orders and fees.

Instead of syncing every individual order, A2X summarises sales by payout period. That means fewer transactions in Xero, but with the same level of detail you’d get manually—only automated and accurate.

Key Features:

  • Connects to Amazon, Shopify, Walmart, eBay, Etsy
  • Handles sales, refunds, shipping, and fees
  • Posts accurate invoices into Xero for each payout
  • Supports multiple currencies and tax rates
  • Used by accountants and bookkeepers globally

Xero eCommerce integrations like A2X are ideal if you sell in high volumes and want reliable, clean bookkeeping without constant adjustments.

If you’re based in the UK or EU, Link My Books is a standout among Xero eCommerce integrations. It’s specifically designed to manage VAT in compliance with HMRC and EU tax regulations—making it ideal for Amazon and eBay sellers in Europe.

Link My Books automatically categorises your transactions by VAT rate, flags zero-rated exports, and prepares accurate accounting entries that match your payouts. It’s one of the few integrations that speaks the language of VAT correctly.

Key Features:

  • Specialised in Amazon, eBay, Etsy, and Shopify
  • Fully MTD VAT-compliant
  • Supports multiple marketplaces and currencies
  • Accountant-friendly and easy to configure
  • Option to map sales by country for OSS/IOSS schemes

For eCommerce sellers concerned about getting VAT wrong, Xero eCommerce integrations like Link My Books are a safety net.

3. Synder: Multi-Payment Gateway Integration

Synder is a robust choice if you need to sync payment data from platforms like PayPal, Stripe, or Square into Xero. Unlike A2X or Link My Books, Synder focuses on the payments side rather than sales marketplaces. It’s perfect for businesses that sell through multiple channels but get paid through a single gateway.

You can sync every transaction or summarise them daily, and Synder matches payouts to your bank feed with precision.

Key Features:

  • Works with PayPal, Stripe, Square, Shopify, WooCommerce
  • Supports US sales tax and UK VAT
  • Multi-currency functionality
  • Detailed reporting and error correction tools

Many online sellers use Synder alongside other Xero eCommerce integrations to complete the picture—sales through A2X or Link My Books, payments through Synder.

4. Shopify + Xero Direct Integration (via Xero App Store)

Shopify has a direct connection with Xero through the app store, but it’s worth noting that this native integration is more basic than specialised tools like A2X. It does sync orders and customer data, but not in the same summarised, reconciliation-friendly format.

Still, for small stores or those just starting out, it can be a helpful way to explore Xero eCommerce integrations without committing to paid tools immediately.

Key Features:

  • Direct order and payment sync
  • Basic tax and fee mapping
  • No summarised sales posting
  • Limited customisation options

It may serve as a stepping stone before you adopt a more advanced integration.

5. WooCommerce + Xero (via WooCommerce Plugins)

If you use WooCommerce, several plugins are available to connect to Xero. Options include plugins by WooCommerce itself, or third-party solutions like Automate.io or Zapier. However, none match the polish of A2X or Link My Books when it comes to reconciliation.

WooCommerce sellers often combine Synder or A2X with a Woo plugin to cover sales and payments.

Xero eCommerce integrations that work with WooCommerce tend to require more setup, but they give you control over mapping products, taxes, and payment methods.

Benefits of Using the Right Xero Integrations for eCommerce

Using the best Xero eCommerce integrations offers several key advantages for online sellers:

1. Accurate Financial Data

No more guessing if Amazon deducted the right fees or trying to split sales by tax rate. Everything is posted properly into your Xero chart of accounts.

2. Time Savings

Instead of spending hours manually entering orders or reconciling PayPal transactions, your accounting runs in the background.

3. Better Decision-Making

With clean data in Xero, you can run profit and loss reports by marketplace, spot underperforming SKUs, and make smarter stock decisions.

4. Tax Compliance

VAT, GST, and sales tax can be difficult in cross-border eCommerce. The right integration helps ensure you’re categorising everything correctly.

5. Audit Trail & Scalability

As your business grows, investors and auditors will want to see a clean trail. These Xero eCommerce integrations help you build confidence from day one.

Which Integration Is Right for You?

Here’s a quick comparison of the top Xero eCommerce integrations mentioned:

ToolBest ForKey MarketplacesTax SupportStarting Price
A2XHigh-volume Amazon/ShopifyAmazon, ShopifyGlobalFrom $19/month
Link My BooksUK/EU sellers focused on VATAmazon, eBayUK, EU VATFrom £13/month
SynderPayment gateway syncPayPal, StripeUS, UK, GlobalFrom $48/month
Shopify NativeSmall Shopify storesShopify onlyBasicFree/Paid
Woo PluginsWooCommerce flexibilityWooCommerceDepends on pluginVaries

Each of these Xero eCommerce integrations brings unique strengths depending on your business model, sales volume, and compliance needs.

How to Get Started

If you’re unsure where to start, begin by identifying your sales channels and how you receive payouts. Then ask:

  • Are your current Xero records messy or inconsistent?
  • Do you need to track VAT, GST, or sales tax?
  • Is reconciliation taking too long?

Most tools offer free trials. Try two or three Xero eCommerce integrations and compare the quality of reports, support, and overall fit.

You may also want to speak to your accountant—many eCommerce accountants already work with these tools and can help you implement them properly.

Final Thoughts

Running an online business involves constant change—new platforms, tax rules, and customer expectations. But one thing remains the same: the need for clear, accurate financial data.

Xero eCommerce integrations aren’t just time-savers; they’re strategic assets. By connecting your storefronts and payment tools with Xero, you create a reliable, professional accounting workflow that supports growth and peace of mind.

Whether you choose A2X, Link My Books, Synder, or another integration, you’re investing in accuracy, clarity, and control.

Need Help Choosing the Right Integration?
As certified Xero specialists, we help eCommerce sellers set up the best Xero eCommerce integrations for their unique needs. Contact us today to book a free consultation.