Shopify Payout Reconciliation — Automatically Fix Missing & Mismatched Payouts
Fincile is a Shopify revenue reconciliation and audit platform that detects missing payments, duplicate charges, refund mismatches, and settlement gaps across Shopify, Stripe, and PayPal. It helps merchants recover lost revenue, verify payout accuracy, and understand their Audit Health Score.
Founding pricing from $39/mo — 14-day free trial, no credit card required.
Sample Merchant Audit
Sample Audit — 30-Day Dataset: $21,117 in Identified Discrepancies Across 3 Issue Types
Why Your Shopify Payouts Never Match Your Bank — And How to Fix It
Shopify Master Orders
This is your source of truth. We use it to verify that every single order processed was actually successfully captured.
Shopify Payments
Essential for detecting Ghost Orders — cases where Shopify says "Paid" but the funds never left the gateway.
Stripe / Gateway Data
This provides actual settlement data. We use it to surface duplicate charges and hidden processor fee leaks.
PayPal Business
PayPal data is notoriously fragmented. This specific export ensures 100% visibility into your actual cash flow.
6 Shopify Payout Problems Fincile Detects Automatically
Missing Payments Detection
Orders marked paid in Shopify with no matching charge in your payment processor. Money that appears settled in your dashboard but never actually arrived in your account.
Duplicate Charge Detection
The same order charged more than once in Stripe or PayPal — caused by retry logic, webhook failures, or payment sync errors that went completely unnoticed.
Refund Verification
Refunds recorded in Shopify that have no confirmed evidence in your processor export. Money that was promised to a customer but may never have been returned.
Settlement Reconciliation
Line-by-line matching of Shopify order totals against gateway payout records to surface amount drift, rounding errors, and systematic settlement gaps.
Processor Fee Analysis
Gateway fee extraction from payout exports so merchants can verify the actual net amount received against the expected settlement value for every order.
Unmatched Payment Detection
Payments received in Stripe or PayPal with no corresponding Shopify order — funds the merchant holds but cannot attribute to any fulfillable transaction.
Built for operators who need clarity fast.
Recover overlooked revenue
Surface discrepancies before they compound across hundreds of orders.
quietly leaving a $500K/month business — from just a 1% reconciliation gap.
Reduce finance clean-up time
Give finance teams a cleaner picture of which transactions reconciled cleanly and which require verification — without manually cross-checking exports across multiple platforms.
Improve merchant confidence
Turn scattered gateway exports into one professional audit view that supports real financial decision-making, investor reporting, and preparation for tax season.
A simple three-step process. Data in, audit out.
Install & Connect
2 minutesInstall Fincile from the Shopify App Store. OAuth connects your store automatically — no manual exports needed. For Stripe, PayPal, and Shopify Payments, live sync pulls your payout data directly via API.
Run an Audit
Select your gateway, set a date range, and click Run Audit. Fincile cross-references every Shopify order against every gateway payout using cent-safe integer math — detecting ghost orders, duplicate charges, refund mismatches, and settlement gaps.
Review Your Findings
Results appear instantly in your dashboard. Every exception shows the exact order ID, amount, and variance. Export findings as CSV or download a PDF audit report — then resolve or dismiss each finding as you go.
Run Your First Audit Free — No Credit Card Required
Install Fincile from the Shopify App Store and run your first full reconciliation audit at no cost. See exactly what your store might be missing before you pay anything.
Questions? Email support@getfincile.com
Your Data Stays Secure
We take data handling seriously, especially for financial data.
Read-Only Processing
Your uploaded files are used only for reconciliation analysis. No write access, no API connections, and no persistent storage of your financial data at any point.
No Storage Policy
Submitted data files are not retained after audit completion. We do not maintain a copy of your Shopify orders or payment records after your report is delivered.
No Third-Party Sharing
Your merchant data is never sold, shared, or used for any purpose beyond delivering your audit report. No exceptions.
Designed for Shopify Merchants With Reconciliation Pain
Growing Stores
Brands processing enough monthly orders that manual reconciliation checking is slow, inconsistent, or simply not happening. If you are processing 200+ orders per month, you need automated verification.
Refund-Heavy Operations
Teams dealing with frequent charge disputes, partial refunds, Buy Now Pay Later complexity, or multiple payment gateways running simultaneously across the same store.
Founders & Finance Leads
Operators who want a definitive answer to whether what Shopify shows as collected actually matches what settled in their bank account — before investors or accountants ask.
Request Your Audit
We'll review your situation and confirm whether Fincile is the right fit for your store.
Send us your contact details and store context
We confirm scope and provide a secure upload link for your files
Audit report delivered within 24 hours of receiving your data
Audit reports delivered within 24 hours of receiving your data
Shopify Payout Reconciliation — Common Questions
Everything Shopify merchants ask about fixing payout mismatches, missing payments, and reconciliation errors.