Reconcile Shopify Payments in Xero — Complete Payout Matching

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Reconcile Complete

Xero Bank Statement Format
valid rows

Reconcile your Shopify Payments in Xero. Match payout transactions to bank deposits, track fees, and close your books accurately.

No API required
Browser-based processing
Run on Google Cloud Platform

Download Sample

Sample payout transactions CSV

Download

Tool Rating

4.8 / 5 (428 votes)

How It Works

1

Export from Shopify

Settings → Payments → View payouts → Select payout → Export transactions

2

Convert

Upload here, select your Xero region and fee options

3

Import to Xero

Import to Shopify Clearing Account in Xero

4

Reconcile

Match bank deposits as transfers from Clearing Account

Why Shopify Reconciliation Is Challenging

The Aggregated Payout Problem

Shopify deposits aggregated amounts to your bank — multiple sales bundled into single payouts. Your bank shows $2,000 deposited, but that's 50 individual orders minus processing fees. Professional bookkeepers solve this with a "Shopify Clearing Account" that receives individual transactions while your bank receives the aggregated payouts.

How This Tool Helps

We convert Shopify Payout Transactions to Xero bank statement format with fee splitting: individual sales as positive amounts, fees as separate negative amounts, refunds as negatives, and payouts for verification. Import to your Shopify Clearing Account in Xero, then reconcile payouts as transfers. When done correctly, the balance should match Shopify's "Available Balance."

Your Data is Safe

Bank-Level Security

256-bit SSL encryption. Same standards as major financial institutions.

No Data Storage

Files are processed directly in browser. No calls to our servers.

GDPR Compliant

Full EU data protection compliance. Your privacy rights protected.

ISO/IEC 27001 Certified GDPR Compliant Swiss Privacy CCPA Compliant

Field Mapping

How Shopify Transactions fields map to Xero Bank Statement

Shopify Transactions Source Value Xero Bank Statement Target Value Note
Type charge → Payee charge Transaction type as payee
Order #1001 → Description #1001 Order reference

Why Use This Tool?

Transaction-Level Detail

Every sale, refund, and fee as individual bank statement lines.

Fee Tracking

Shopify payment processing fees extracted as separate expense rows.

Payout Matching

Match individual transactions to aggregated bank deposits.

Month-End Ready

Clearing account should zero out when all payouts are matched.

Audit Trail

Order numbers preserved for tracking back to Shopify.

Browser Processing

Financial data processed locally. Never sent to external servers.

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Common Bank Statement Import Errors

Issues you might encounter when importing Payouts/Transactions data to Bank Statement - and how we solve them

Invalid Date Format

Xero requires regional date format

Select correct region in processing options

Re-export with correct region setting

Incorrect Amount Sign

Fees should be negative in bank statements

We automatically invert fee signs

Verify amounts during reconciliation

Frequently Asked Questions

Create a new bank account in Xero (Accounting → Bank Accounts → Add Bank Account). Name it 'Shopify Payments' and select 'Other' as the account type. This acts as a holding account for Shopify transactions.
Separating fees lets you track your actual processing costs as expenses. Your revenue is recorded at the gross amount (matching your 1099-K), while fees reduce your profit as expenses rather than reducing revenue.
After processing all transactions and matching all payouts, your Shopify Clearing Account balance in Xero should match Shopify's 'Available Balance' in Settings → Payments. Any difference indicates missing transactions.
Pending payouts haven't been deposited yet. Only reconcile transactions from completed payouts that have actually hit your bank account.
Most businesses reconcile monthly at month-end. Import all transactions from the month, match to bank deposits, and verify the clearing account balance.

Shopify → Xero Data Ecosystem

All available data flows from Shopify to Xero

Shopify Customers Export Customer profiles with contact info, addresses, and marketing preferences
→
Xero Contact Customer or supplier contact records
First Name + Last Name → Name First Name → FirstName Last Name → LastName
Customer sync, supplier management
Shopify Orders Export Customer orders with line items, shipping, taxes, discounts, addresses
→
Xero Sales Invoice Sales invoices for accounts receivable (B2B, payment terms)
Name → InvoiceNumber Name → Reference Created at → InvoiceDate
B2B sales, invoiced orders, payment terms
Shopify Payouts/Transactions Shopify Payments transactions, fees, and bank deposits
→
Xero Bank Statement Bank transactions for reconciliation
Transaction Date / Payout Date → Date Amount / Net → Amount Type → Payee
Payout reconciliation, fee tracking Current tool
Shopify Products Export Product catalog with variants, pricing, inventory, and images
→
Xero Inventory Item Products and services for inventory tracking
Variant SKU / Handle → ItemCode Title + Option Values → ItemName Body (HTML) → Description
Product catalog sync, inventory management
Shopify Refunds (via Orders Export) Refunded orders filtered from Orders export. Filter by Financial Status = refunded.
→
Xero Credit Note Refunds and returns as credits against invoices
Name + '-R' → CreditNoteNumber Name → Reference Created at → CreditNoteDate
Refund processing, returns handling