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.
Beyond Reconciliation — In Active Development
These features are being built right now and are not yet available in the live app. We're listing them here so you know where Fincile is headed — not as a claim about what it does today.
Chargeback Defense
Automatically assemble evidence from your real transaction data and submit it directly to Stripe, PayPal, Braintree, Razorpay, Afterpay, and Shopify Payments — no manual dispute paperwork.
Gateway Fee Audits
Catch processor fees that drift from your contracted rate before they quietly eat into your margin, order after order.
Duplicate & Fraud Interception
Flag suspicious duplicate charges as they happen, using your own store’s transaction patterns — not a one-size-fits-all rule.
Revenue Recovery Engine
Review and approve a fix once — a duplicate refund, an order correction — and Fincile executes it safely, then confirms it actually went through with the gateway itself.
No-Ledger UX
See money earned, money missing, and money cleared in plain English — no spreadsheet, no accounting background required.
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 Shopify Access
Fincile connects via Shopify OAuth with read-only access to your orders — never write access to your store, and no customer or payment-terms data requested. Gateway credentials (Stripe, PayPal) are encrypted with AES-256 before storage and never exposed in responses.
Your Audit History, Your Control
Your audit history and findings are retained in your dashboard so you can review them anytime — retention depends on your plan (3 months on Starter, 12 months on Growth, unlimited on Scale+). Request full deletion anytime at support@getfincile.com.
No Third-Party Sharing
Your merchant data is never sold, shared, or used for any purpose beyond delivering your reconciliation reports. 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.