Fix Shopify and Stripe in Xero, the simplest native setup for clean payouts
Set up Xero’s native Shopify app and Stripe in minutes, use clearing accounts, match payouts in one click, avoid duplicates, and handle US sales tax correctly. Updated September 19, 2025.
Updated September 19, 2025
If your Shopify or Stripe payouts never match your sales, fees, and refunds, this guide shows the simplest native Xero setup. You will connect Shopify and Stripe, use clearing accounts correctly, and reconcile payouts in one click without duplicates.
Quick Start
- Install Shopify integration by Xero and connect your store.
- In the app settings, map Sales, Discounts, Shipping, Refunds, Gift cards, and Fees. Accept the clearing account.
- Optional backfill. Import up to 90 days of Shopify history on first connect if you need it.
- In Xero, go to Settings → Payment services, add Stripe, and connect your payout bank.
- Let the daily Shopify summary post to the Shopify clearing account.
- When payouts land in your bank feed, Xero suggests a match to transfers and fees. Click OK.
- After month end, set a Lock date so past reconciliations stay fixed.
Key facts
- Shopify → Xero posts one daily summary that includes sales, discounts, shipping, refunds, gift card payments, and fees.
- The app uses a clearing account per gateway and posts transfers to your bank for easy matching.
- You can import up to 90 days of previous Shopify sales on first connect with Standard or Premium plans.
- US sales tax filing is handled from Shopify tax reports, not from the native Xero app.
- Stripe + Xero will usually auto match payouts to payments and fees. You click OK in Reconcile.
What you need
| Thing | Why it matters |
|---|---|
| Xero org (US), Standard or Premium if you want backfill | Unlocks 90‑day Shopify import on first connection. |
| Shopify admin with permission to manage and install apps | Required to install and configure the Xero Shopify app. |
| Stripe account with automatic payouts to your US bank | Enables one‑click payout matching and fee accounting in Xero. |
| Bank feed in Xero | Lets you reconcile real deposits against transfers from the clearing account. |
| Xero user role: Standard or Adviser | Only these roles can connect apps. |
Still choosing accounting software? Read Xero vs QuickBooks: Which Accounting Software is Right for Your Business?.
Step‑by‑step setup
A) Shopify → Xero
- Open the Shopify integration by Xero and click Get this app, then choose your Xero organization.
- In the integration Settings, map accounts:
- Sales → Sales revenue
- Discounts → Discounts given (contra revenue)
- Shipping → Shipping income or shipping expense
- Refunds → Returns or refunds account
- Gift cards → Revenue or liability per your policy
- Fees → Merchant fees expense The app will create or use a clearing account for each gateway.
- Optional backfill. Import up to 90 days during first connection.
- Let it run. It posts daily summaries and shows fees, discounts, shipping, refunds, gift cards across invoices, then transfers processed sales into your bank for fast reconciliation.
New to Xero? Our Xero Review: The Best Cloud Accounting Software for Small Businesses? covers features, pricing, and real pros and cons.
B) Stripe → Xero
- In Xero, go to Settings → Payment services → Add Stripe, then Connect to Stripe and select your payout bank account.
- When Stripe pays out, Xero will usually match the bank deposit with the Stripe payments and fees it recorded. Click OK. If no match is suggested, use Find & Match.
How the money flows
- Orders happen in Shopify.
- The daily summary lands in Xero and posts to a Shopify clearing account with sales, discounts, shipping, refunds, gift cards, and fees.
- The app posts a transfer from clearing to bank for processed sales, matching your bank feed deposit.
- Stripe payouts appear in the bank feed. Xero auto matches to payments and fees. You click OK.
Daily reconciliation checklist
- Open Accounting → Reconcile.
- Look for a green match on each Shopify or Stripe payout line.
- If needed, click Find & Match and select the transfer or related lines.
- Confirm the clearing account trends back toward zero after each payout.
- Review any negative days. Refunds and fees can straddle payout dates.
- After month end, set a Lock date to prevent changes to past periods.
Recommended account mapping
| Shopify element | Suggested Xero mapping | Notes |
|---|---|---|
| Sales | Sales revenue | Primary income |
| Discounts | Discounts given (contra revenue) | Keeps revenue net clean |
| Shipping | Shipping income or shipping expense | Pick one policy and stick to it |
| Refunds | Returns or refunds account | Shows as negative on daily summary |
| Gift card payments | Revenue or liability | Be consistent across periods |
| Fees | Merchant fees expense | Stripe, Shopify Payments, PayPal fees |
| Clearing | Bank‑type clearing account | Used by the app to hold daily totals |
Troubleshooting in one page
- No auto match for Stripe payout. Confirm Stripe is connected as a payment service to the same bank, then use Find & Match once. Future matches usually stick.
- Duplicate payouts. Do not create manual Receive Money if the app already posted a transfer. Keep one source of truth and match the bank line to the transfer.
- History missing. Shopify backfill is up to 90 days on first connect. Older periods need manual summaries or a separate import.
- US sales tax. Handle and file from Shopify. The native app does not create US tax returns.
- Past periods changing. Set Lock dates so reconciled months cannot be edited.
Verification test
- Place a small order in Shopify.
- Wait for the daily summary to arrive in Xero.
- When the Stripe payout lands, reconcile the bank line by matching to the transfer or suggested items. Click OK.
- Check the clearing balance returns toward zero.
FAQ
Do I need a clearing account and what type
Yes. The app adds a clearing account for gateways and posts transfers into your bank. Treat it as a bank‑type account with no feed.
How much history can I import
On first connect you can import up to 90 days on Standard or Premium.
How are refunds handled
Refunds appear as negative lines on the daily summary that reduce the day total. Reconcile the net payout. Chargebacks are posted and reconciled manually when they appear.
Will Xero match Stripe payouts automatically
Usually yes. Xero will match payments and fees to the bank line. Click OK to accept.
Does the native app file US sales tax
No. File from Shopify’s tax reports.
How do I keep past months from changing
Set Lock dates in Xero after month end.
