Running Shopify on Xero sounds simple, but sellers quickly discover it isn’t. Each payout bundles sales, refunds, shipping, discounts, fees, and tax into one figure that rarely matches the deposit in your bank. Reconciling this manually means CSV exports, tax guesswork, and hours spent forcing numbers to balance.
Xero does offer a direct Shopify integration, but in practice, it often posts incomplete or inaccurate data. Fees, refunds, and tax lines are frequently missing, which means payouts in Xero don’t match your bank feed. Instead of solving the problem, the native integration creates more manual work.
That’s why many sellers look to automation tools. A2X and Link My Books both connect Shopify to Xero, summarizing payouts and posting them correctly so reconciliation takes minutes instead of hours. But how they do it (and how much they cost) can be very different.
Key Takeaways from this Post
Shopify’s native Xero integration creates reconciliation headaches.: It often misses fees, refunds, and tax details, meaning payouts in Xero rarely match bank deposits.
A2X and Link My Books both automate payout summaries, but the experience differs: A2X handles Shopify Payments cleanly but relies on clearing accounts for PayPal and other gateways, adding manual steps.
For multi-channel and VAT-registered sellers, Link My Books is the smarter long-term choice: It supports more platforms under one plan, applies VAT and OSS rules automatically, and costs 30–40% less than A2X’s per-channel.
Common Problems Shopify Sellers Face Integrating With Xero
Xero offers a direct Shopify integration, but many sellers find it creates more problems than it solves. The app often posts incomplete or inaccurate data, leaving out key details like fees, refunds, and taxes. This means payouts in Xero rarely match what hits your bank, forcing manual corrections and making reconciliation unreliable.
💡 This is why most growing Shopify businesses turn to dedicated tools like A2X or Link My Books to get accurate summaries that tie out perfectly in Xero.
Overview of A2X and Link My Books for Shopify sellers
Both A2X and Link My Books automate Shopify-to-Xero bookkeeping, but they approach it differently.
A2X connects Shopify to Xero by summarizing each payout. It captures sales, refunds, shipping, fees, and taxes, then posts them into Xero as draft invoices or journals that match your bank deposits . For Shopify Payments, this means one-click reconciliation. For PayPal and other gateways, A2X uses clearing accounts so that deposits can be reconciled correctly . A2X also includes COGS tracking if SKU and cost data are provided, so you can calculate gross profit margins accurately .
Link My Books takes the same payout-summary approach but was designed with UK and EU sellers in mind. It applies the correct VAT and OSS rules automatically, separates zero-rated sales, and prevents common overpayment errors. Pricing is based on order volume rather than per channel, making it more cost-effective for multi-channel sellers. The setup wizard guides you through account and tax mappings, and UK-based accountants are available for onboarding support.
In short, both tools replace spreadsheets and manual reconciliation, but the experience differs: A2X often needs more manual configuration, while Link My Books emphasizes faster setup, VAT compliance, and lower costs for sellers running multiple sales channels.
TL;DR: A2X vs Link My Books for Shopify
💡 Both automate Shopify bookkeeping, but Link My Books is built around VAT compliance and better value for multi-channel sellers. A2X is accountant-friendly, strong for payout summaries, but more costly if you sell on multiple platforms.
What most Shopify sellers don’t consider with the A2X & Xero Integration
Shopify Payments vs other gateways
- For Shopify Payments, A2X generates a draft invoice (or journal) that corresponds to the Shopify Payments payout in Xero, making reconciliation with the bank feed smoother.
- For PayPal and other gateways, A2X uses a clearing account (e.g. “PayPal Shopify Clearing”) in the accounting system. This is a current asset account used to track funds in transit or expected deposits; it helps match gateway payouts that don’t align exactly with what appears in the checking account due to timing or deductions (e.g. processing fees).
- The clearing account requires manual mapping/matching in some cases; transactions may sit in the clearing account until they are deposited and reconciled in the bank.
Free trial limits
- A2X’s free trial allows you to fetch the last 5-10 payouts from your connected e-commerce platform.
- During the trial, you can review only the last three payouts, and you are limited to posting three of those as entries into your accounting system (e.g. into Xero).
- There is no fixed expiry time for the free trial - you can stay in free trial mode until you decide to subscribe.
COGS setup
- A2X supports COGS (Cost of Goods Sold) tracking for Shopify stores, but this works properly only when SKUs / item cost data are set up and entered correctly in Shopify / in the product data. Without that, COGS won’t be accurate.
- The posting of COGS is included in A2X’s Shopify pricing plans (e.g., the plans from $29/month up depending on order volumes) where COGS is a listed feature.
Pricing by channel / Multi-channel implications
- A2X pricing starts at US$29/month for the Shopify plan. That covers a single channel/store, certain order-volumes, etc.
- For sellers using multiple channels or stores, A2X offers Multi-channel pricing plans that allow you to connect multiple channels. These plans cost more depending on the combined number of orders and channels.
- Because each additional channel increases complexity (and the cost in multi-channel plans), sellers may underestimate how much they’ll end up paying when they add stores or marketplaces beyond a single Shopify store.
Features Compared
Both A2X and Link My Books aim to simplify Shopify-to-Xero bookkeeping, but the way they handle tax automation, reconciliation, reporting, and pricing can be very different. Below we break down the core features side by side so you can see where each tool shines, and where one falls short.
A2X vs Link My Books: Tax Automation
Link My Books
- Built for UK/EU sellers where VAT rules are complex.
- Automatically applies VAT codes and OSS logic, separating standard-rated, reduced-rated, and zero-rated sales.
- Prevents common errors that lead to VAT overpayments.
A2X
- Supports VAT, GST, and sales tax mapping across jurisdictions.
- Shopify Payments tax is included in payout summaries, but advanced mapping may require an accountant to configure correctly .
- Marketplace Facilitator Taxes (MFV) are identified, but sellers remain responsible for assigning correct tax codes in Xero.
💡 Bottom line: Link My Books is plug-and-play for VAT; A2X offers global tax support but requires more manual setup.
A2X vs Link My Books: Reconciliation & Gateways
Link My Books
- Payout summaries from Shopify and all gateways (PayPal, Stripe, etc.) are imported and matched directly to Xero bank feeds.
- No clearing accounts needed. You can reconcile your Shopify payments in one click.
A2X
- For Shopify Payments, you can also reconcile in one click.
- For PayPal or Stripe, A2X posts to gateway clearing accounts. These balances must then be cleared manually when deposits hit the bank .
A2X vs Link My Books: COGS Tracking
Link My Books
- Automatically calculates COGS at the SKU level, included in all plans.
- Provides gross profit visibility without extra setup.
A2X
- Offers SKU-level COGS, but only if product SKUs and cost data are correctly maintained in Shopify.
- Posts COGS as monthly journals, not per payout .
- 💡 Bottom line: both tools can track COGS, but Link My Books includes it by default and aligns it with payout reconciliation.
A2X vs Link My Books: Reporting & Insights
Link My Books
- Built-in performance analytics and industry benchmarking for e-commerce sellers.
- Lets you compare sales and margins against industry averages.
A2X
- Focused on payout summaries and accounting accuracy.
- Does not provide benchmarking or financial performance dashboards.
💡 Bottom line: Link My Books adds analytics beyond bookkeeping. A2X sticks to clean accounting summaries.
A2X vs Link My Books: Integrations
A2X
- Supports accounting integrations with Xero, QuickBooks Online, Sage, and NetSuite.
- Connects to major e-commerce platforms: Shopify, Amazon, Etsy, eBay, Walmart, and BigCommerce.
- Payment processor coverage includes Shopify Payments, PayPal, and others.
Link My Books
- Connects with Xero and QuickBooks Online, covering the two dominant choices for Shopify sellers.
- E-commerce integrations include Shopify, Amazon, eBay, Etsy, TikTok Shop, Walmart, Square, and WooCommerce.
- Also integrates with key payment processors like PayPal and Klarna.
Where Link My Books excels: broader e-commerce coverage, including TikTok Shop, which is rapidly expanding as a marketplace.
Where A2X excels: a wider range of accounting software, supporting Sage and NetSuite.
Link My Books overview
Link My Books was built specifically for e-commerce sellers who use Shopify with Xero or QuickBooks. Instead of forcing you to untangle CSVs and tax codes manually, it automates the entire bookkeeping process.
From VAT handling to SKU-level COGS, it posts clean payout summaries that match your bank deposits every time. Because pricing is based on order volume rather than channels, it’s also one of the most affordable tools for multi-channel sellers who want scalability without hidden costs.
Here’s what to expect:
Automated Payout Reconciliation
Link My Books imports Shopify payouts directly, breaking them down into sales, refunds, fees, shipping, and tax. It then creates summary invoices in Xero that match your bank deposits line for line. This eliminates manual CSV uploads and ensures reconciliations are accurate every month.
Built-in VAT Handling
Designed for UK and EU sellers, Link My Books automatically applies VAT and OSS rules. Standard-rated, reduced-rated, and zero-rated sales are separated correctly, preventing the common mistake of overpaying VAT. This feature is especially important for sellers above the £85k UK VAT threshold.
Cross-Channel Reporting
Link My Books isn’t limited to Shopify. You can connect Amazon, eBay, Etsy, TikTok Shop, Square, Walmart, and WooCommerce alongside your Shopify store. The tool gives you Profit & Loss visibility per channel, so you can see which platforms are most profitable and make informed scaling decisions.
Financial Insights & Benchmarking
Beyond reconciliation, Link My Books offers industry benchmarking and financial summaries. You can compare refund rates, fees, and margins against other sellers, spot low-performing platforms, and track profitability in real time.
Positives of Link My Books
- Tailored for VAT compliance: With workflows designed by UK-based accountants, Link My Books handles EU VAT complexities that generic accounting tools often miss. It’s a major safeguard for sellers navigating OSS and cross-border rules.
- Multi-channel friendly pricing: Pricing is based on monthly order volume, not the number of sales channels. This means you can connect Shopify, Amazon, and TikTok Shop under one plan without paying for multiple subscriptions.
- Ease of use: The setup wizard walks you through account mapping and tax codes step by step. Even without deep accounting knowledge, most sellers can get started in under 15 minutes, with optional onboarding calls available.
Downsides of Link My Books
- Learning curve during setup: Sellers who have never dealt with VAT or bookkeeping may still prefer to involve their accountant for the initial configuration.
- Historical data limit: Access to older transactions depends on your plan (e.g., 12–24 months). If you need longer history imported, you may need to upgrade or you can purchase extra historical data beyond the default 3 months if needed.
Link My Books pricing
Our pricing is now flexible and scales with your business based on two factors:
- Monthly order volume: whether you process 200 orders or 250,000 orders, you only pay for what you use.
- Number of connected sales channels: one Shopify store, or multiple stores across Amazon, Etsy, TikTok Shop, and eBay.
Check out our price calculator to see where you would land.
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Every subscription includes:
- Unlimited users (ideal for accountants or teams)
- Free onboarding with a qualified accountant
- Built-in VAT and OSS automation
- SKU-level COGS tracking
- Industry benchmarking and profitability insights
- A 14-day free trial with no credit card required
This flexible pricing model makes Link My Books especially attractive for multi-channel sellers, since you’re not forced into separate subscriptions for each marketplace. Instead, you simply pay for your total order volume and number of channels - often saving hundreds or even thousands compared to A2X.
A2X overview
A2X is a long-standing tool for e-commerce accounting that connects Shopify with Xero, QuickBooks, Sage, and NetSuite. Its core strength lies in creating payout summaries that include sales, refunds, fees, shipping, and tax, which are sent to Xero as draft invoices or journals for reconciliation.
For Shopify Payments, this process is straightforward, but with PayPal and other gateways, A2X relies on clearing accounts, which can add complexity. It also supports VAT, GST, and sales tax mapping, along with SKU-level COGS tracking via monthly journals. While accurate and flexible, A2X pricing is calculated per channel, making it more expensive as sellers expand to multiple marketplaces.
Here’s what to expect:
Payout Summaries for Xero
A2X takes Shopify payouts and summarizes them into invoices or journals that capture sales, refunds, shipping, fees, and taxes. These summaries are sent to Xero as drafts, ready to be approved and reconciled with your bank feed .
Handling Gateways with Clearing Accounts
For Shopify Payments, payouts can reconcile directly in Xero. For other gateways like PayPal or Stripe, A2X posts transactions into clearing accounts. These balances then need to be cleared when deposits appear in your bank feed .
Tax Mapping
A2X supports VAT, GST, and sales tax handling. Taxes are included in payout summaries, and A2X identifies Marketplace Facilitator Taxes (MFV). Sellers are responsible for mapping tax codes correctly in Xero .
COGS Tracking
A2X can calculate Cost of Goods Sold if SKUs and cost data are set up correctly. It posts COGS journals monthly, helping sellers see gross profit margins more accurately .
Positives of A2X
- Accurate payout summaries: Replaces manual CSVs with summaries that line up with Shopify payouts, reducing reconciliation errors.
- Global tax flexibility: Handles VAT, GST, and sales tax across multiple jurisdictions, making it useful for international sellers.
- Accounting software coverage: Works not only with Xero and QuickBooks Online, but also Sage and NetSuite - giving more options to larger or more complex businesses.
What could be better
- Extra steps for non-Shopify gateways: PayPal and Stripe require clearing accounts, adding complexity compared to direct reconciliation.
- No built-in financial insights: A2X’s focus is on syncing accurate data into your accounts. It does not provide business benchmarking or profitability dashboards - those must be built in Xero or third-party tools.
- Pricing structure: A2X charges per channel. Sellers with multiple stores or marketplaces must either pay for separate plans or upgrade to a multi-channel plan, which increases costs .
A2X pricing
- Shopify single-channel plans start at US$29/month (Mini plan, up to 200 orders) and scale with order volume (e.g. 1,000 orders = US$69/month; 5,000 orders = US$139/month) .
- Multi-channel plans cover more than one platform (Shopify, Amazon, eBay, etc.) and scale based on both order volume and the number of connected channels .
- Free trial includes the last 5–10 payouts, with up to 3 entries posted into Xero before a subscription is required .
💡 A2X is best for Shopify sellers who want accurate payout summaries and flexibility across multiple accounting platforms. Costs, however, can rise quickly for multi-channel businesses.
Link My Books vs A2X Pricing (2025)
💡 Summary: Link My Books’ dynamic model scales with your order volume and channels, while A2X locks you into separate subscriptions or multi-channel tiers. For most Shopify sellers, especially those expanding across platforms, LMB is consistently cheaper and simpler.
A2X or Link My Books: Which should you choose?
Both A2X and Link My Books solve the same core problem: turning messy Shopify payouts into clean entries in Xero. But once you look closely at setup, VAT handling, reporting, and - most importantly - pricing, the differences become clear.
Recommendation
- Choose A2X if: you need compatibility with Sage or NetSuite, or you’re an accountant who prefers very granular control over payout summaries.
- Choose Link My Books if: you’re a Shopify + Xero seller who wants fast setup, automated VAT compliance, and lower costs as you grow across channels.
💡 With its new dynamic pricing model, Link My Books is consistently cheaper and more flexible than A2X. Multi-channel sellers especially benefit, since there are no hidden per-channel fees. For most Shopify + Xero users, Link My Books is the smarter choice: accurate reconciliation, VAT compliance baked in, and pricing that scales fairly with your business.
Frequently Asked Questions
How does A2X connect Shopify to Xero?
A2X summarizes each Shopify payout into invoices or journals that include sales, refunds, fees, shipping, and taxes. These are posted as drafts in Xero so you can approve and reconcile them against your bank feed. For a simpler approach, check out our guide on Shopify Xero reconciliation.
Does A2X handle PayPal and Stripe payments from Shopify?
Yes, but with extra steps. Shopify Payments payouts reconcile directly in Xero, while PayPal, Stripe, and other gateways use clearing accounts. This means funds sit in a clearing account until deposits hit your bank, adding another reconciliation step. Link My Books handles this automatically as part of Shopify bookkeeping.
Can A2X track Cost of Goods Sold (COGS) for Shopify?
Yes. A2X can generate monthly COGS journals if SKUs and cost data are set up correctly in Shopify. Without SKU-level costs, COGS reporting won’t be accurate. Link My Books includes automatic SKU-level COGS in all plans, making it the smarter choice for Shopify accounting software.
Does Link My Books handle VAT automatically?
Yes. Link My Books was built for UK/EU sellers and automatically applies VAT, OSS, and zero-rated logic. This prevents common VAT overpayment errors. You can read more in our Shopify VAT guide.
What’s the difference in pricing between A2X and Link My Books?
Link My Books starts at £17/month (~US$21) for 200 orders, with pricing based on order volume and no per-channel fees.
A2X starts at US$29/month for 200 orders on a single channel. Multi-channel plans cost significantly more, with the 10K Multi plan priced at US$229/month.
For a breakdown of alternatives and savings, see our full guide to A2X alternatives.
Which tool is better for multi-channel sellers?
Link My Books. Its pricing covers multiple channels under one subscription, while A2X requires separate plans or expensive multi-channel tiers. Sellers running Shopify + Amazon + eBay often save over US$1,000/year with Link My Books.
Can accountants use both tools?
Yes. A2X integrates with Xero, QuickBooks, Sage, and NetSuite, which appeals to accountants serving diverse clients. Link My Books focuses on Xero and QuickBooks, but offers unlimited users per account, making it cost-effective for accountants managing multiple e-commerce clients.
Streamline your Shopify accounting with Link My Books
Manually reconciling Shopify payouts in Xero wastes hours each month and increases the risk of errors or VAT overpayments. While A2X offers a solution, its per-channel pricing and extra steps for non-Shopify gateways can quickly add complexity and cost.
Link My Books is the easier way:
- Connect Shopify and Xero in minutes.
- Let the setup wizard map accounts and VAT automatically.
- Sync accurate payout summaries that match your bank deposits perfectly.
- Get real-time Profit & Loss by channel and benchmark your performance.
👉 Start your free trial and see why sellers are switching from A2X every day.
Join thousands of e-commerce sellers who trust Link My Books to keep their accounts clean, compliant, and scalable.
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