To connect Shopify to Xero, most stores use the Shopify Xero integration that Xero makes, called the Shopify integration by Xero. It is free on all Xero plans and is built for Xero by Amaka. Once a day it brings your Shopify sales and fees into Xero, as one summary or one entry per order, and moves each payout to your bank account. You can also use a payout app like A2X or a Zapier zap. Where they stop: fees for a whole day land as one line, US sales tax is not handled, and someone still has to check each deposit against the orders inside it. AI agents do that check and tell your bookkeeper what doesn't match.
What a Shopify Xero integration has to do
Your sales live in Shopify. Your books live in Xero. A Shopify payout is not one sale. It is many orders, minus Shopify's fees and any refunds. If nobody links them, your bookkeeper adds it up by hand and hopes the deposit matches.
So a good connection does two things. It puts each sale, fee, refund and tax amount in the right account in Xero. And it checks each deposit against the orders inside it, so your bookkeeper only looks at what is off.
Three ways to connect Shopify and Xero
Most stores start with the first one. The other two fill gaps it leaves.
The Shopify integration by Xero
- How it works
- You add it from the Xero App Store. Xero's help says it is free and built by Amaka. Each day it brings your online store and Shopify POS sales into a Shopify Payment Balance account in Xero, as invoices or as bank transactions, and records fees as spend money. When Shopify sends a deposit, Xero makes a transfer to your bank account for you to reconcile.
- Good for
- Stores that want daily sales, fees and payouts in Xero without typing them in.
- Where it breaks
- Fees for each 24 hours come across as one line, even when you sync per order. Xero's US page says the integration does not account for US sales tax, so you still download that from Shopify. On the Ignite plan you can bring in only 20 invoices a month. It goes back only 90 days.
A payout app like A2X
- How it works
- A2X is listed in the Shopify App Store as A2X Sync for QuickBooks and Xero. It groups each payout's sales, fees, taxes, refunds and gift cards into one summary in Xero that matches the deposit.
- Good for
- Stores with many orders a day, and bookkeepers who think in payouts.
- Where it breaks
- It is a separate subscription from Xero. You get one summary for each payout, so Xero doesn't hold the detail of each order or customer. Other apps in this space get mixed reviews: Amaka's own paid sync app in the Shopify App Store is rated 2 out of 5, with reviews about failed syncs that had to be entered by hand.
A Zapier zap
- How it works
- Zapier can turn a new paid Shopify order into a Xero sales invoice, a payment or a credit note. You build each step yourself.
- Good for
- Small stores with a few orders a day and one way to get paid.
- Where it breaks
- Refunds, discounts, shipping, tax and fees are each a step you build. Miss one and the books drift, and a zap that fails doesn't tell your bookkeeper.
Arkeo agents
- How it works
- Agents read each day's orders, refunds and payouts in Shopify, check what came into Xero, and match each payout to the orders in it and the deposit in your bank.
- Good for
- Stores where Xero has to match the bank, and nobody has the hours to check.
- Where it breaks
- Anything your rules keep for a person, like a large refund or a payout it can't match, goes to your team in one message.
How to set up the Shopify Xero integration
These follow Xero's own help article for the Shopify integration. Open it for the screens.
- 1Add the app from the Xero App Store
In Xero, click your organisation name, then Xero App Store. Find Shopify, click Get this app, select your organisation and click Allow access. Then click Connect to Shopify and Grant access.
- 2Select Simple or Advanced setup
Simple makes default accounts and tax types for you. Advanced lets your bookkeeper map sales, discounts, shipping, fees, chargebacks, tips and gift cards to your own accounts. Ask your bookkeeper first.
- 3
Set how sales come across
Under Sales Sync, select Summarised for one entry a day, or Per Order for one entry per sale. Then select Invoice or Bank Transactions. On the Ignite plan, use Bank Transactions, since it allows only 20 invoices a month.
- 4Map taxes and the payout bank account
Map Shopify's taxes to your Xero tax rates. Next to Shopify Payment Balance, select the bank account your payouts land in. If you sell in the US, plan to pull sales tax from Shopify for filing.
- 5Set the start date, then check one week
Bring in up to 90 days of past sales, set Start sync data from, and save. After a week, compare each Shopify payout to the transfer in Xero, line by line.
Where the Shopify Xero integration stops
The integration moves the sales. The work in the middle is still yours.
Fees and payouts come across in bulk. Xero's help says all fees for a 24-hour period sync as one transaction, even when each sale comes across on its own. One Shopify payout holds many sales, minus refunds and chargebacks. So the transfer Xero makes and the deposit in your bank are not always the same number, and someone has to find out why.
Some things don't come across at all. Xero's US page says the integration does not account for US sales tax, and that sales tax data has to be downloaded from Shopify for reporting and filing. Past sales go back only 90 days. If you change the bank account your payouts go to, you have to change it in Shopify, not Xero.
And your plan can get in the way. On Xero's Ignite plan you can bring in only 20 invoices a month, so a store that syncs per order as invoices runs out fast.
The apps that fill these gaps have their own trouble. Amaka's own paid Shopify sync app is rated 2 out of 5 in the Shopify App Store. Its 2026 reviews talk about syncs that failed and had to be entered by hand, tax that didn't sync, and support that was hard to reach.
The agents that do it
Each agent does one job from start to finish, in your own Shopify and Xero. Your team talks to them in Slack or Teams.
Know what sold without building the report.
- Pulls sales, refunds and top productsevery Monday
- Compares it to last weekevery Monday
- Sends it to your teamMonday morning
Bills in Xero without typing them in.
- Reads supplier bills from emailas they come
- Enters each bill as a draft in Xerosame day
- Sends it to the owner to approveright away
Questions
Is my customers' information safe?
Yes. Agents work in your own Shopify and Xero and see only what their job needs. Customer details never go into public AI. Agents connect to AI through business-grade connections audited under SOC 2.
Is the Shopify integration by Xero free?
Yes. Xero's App Store listing says it is free on all Xero plans. Apps from other makers, like A2X, charge their own fees.
Should I sync a daily summary or each order?
A daily summary keeps Xero light, and Xero suggests it for busy stores. Per order gives you the customer and line items for each sale. Either way, fees for the day come across as one line.
Does the Xero Shopify integration handle sales tax?
It maps Shopify's taxes to your Xero tax rates. But Xero's US page says it does not account for US sales tax, so US stores download sales tax data from Shopify for filing.
What does it cost?
You get the price on the call, along with the hours it saves your team.