What is Shopify vs PSP reconciliation?

It is the process of comparing Shopify order, payment, refund, and sales records with PSP payment, fee, refund, dispute, settlement, and payout reports to identify matched records, amount differences, deductions, and open items.

What files are required?

The main files are usually the Shopify order report and PSP payment report. Depending on the workflow, refund, fee, dispute, settlement, payout, bank, ERP, books, or supporting data files may also be used.

Which PSPs can this workflow support?

This workflow can support PSP or payment gateway reports such as Stripe, PayPal, Razorpay, Cashfree, PayU, Shopify Payments, or other payment providers, depending on the available report format and required matching logic.

Can Cointab reconcile Shopify refunds?

Yes. Shopify refund data and PSP refund data can be included in the workflow so the team can review whether refunds, cancellations, returns, and customer credits are correctly reflected.

Can Cointab identify PSP fees and deductions?

Yes. Where fee, tax, adjustment, dispute, currency conversion, or deduction data is available in the reports, Cointab can use it to explain payout differences.

Can Cointab reconcile disputes and chargebacks?

Yes. Dispute, chargeback, reversal, and dispute fee records can be included so finance teams can review their impact on sales, receivables, and payouts.

Can Cointab compare PSP payouts with bank receipts?

Yes. If bank statement data is added, Cointab can compare PSP payout records with actual bank credits and identify bank receipt differences.

Can I reuse this reconciliation every month?

Yes. Once this template is selected and the workflow is used, the same setup can be reused for future periods.

Can this run automatically?

Yes. Once configured, Cointab can receive or pull required reports through email, SFTP, or APIs where available, run reconciliation automatically, and push output back to downstream systems.

What if my Shopify or PSP report format is different?

Cointab validates uploaded files against the expected format. If the file format is different, users can correct the file, update the workflow, or create a custom reconciliation.

Can AI help with Shopify PSP reconciliation?

Yes. AI can help match difficult open transactions, review messy references, analyze exceptions, and suggest possible reasons and next actions.

Can I manually match Shopify and PSP transactions?

Yes. Users can manually match transactions that the system and AI could not confidently match, and undo manual matches if needed.

Can I download the Shopify PSP reconciliation report?

Yes. Users can download Excel reports with fully matched, partially matched, unmatched, skipped, and transaction-level details.

Popular reconciliation template

Shopify vs PSP Reconciliation

Reconcile Shopify orders with PSP payments, refunds, fees, disputes, settlements, and payout reports in one structured workflow.

Upload your Shopify and PSP reports, select the period, run reconciliation, and review fully matched, partially matched, unmatched, and skipped records.

Start this reconciliation Schedule guided setup

View demo report

Ready-made workflow · Reusable every period · Manual upload or automated data flow

Shopify Orders

PSP Payments

Refund / Dispute Data

Settlement / Fee Data

Cointab Shopify PSP Reconciliation

MatchedPartially MatchedUnmatchedSkipped

Reconcile Shopify sales with PSP payments and payouts

Shopify and PSP reports can include orders, payments, refunds, fees, disputes, settlements, adjustments, and payout amounts. Cointab helps bring these into a clear reconciliation report.

The Shopify vs PSP reconciliation helps finance teams compare Shopify order records with payment, refund, settlement, and payout data received from payment service providers.

This helps finance teams answer questions such as:

Which Shopify orders were successfully paid through the PSP?
Which Shopify orders are missing in the PSP payment report?
Which PSP payments do not have a matching Shopify order?
Which refunds, disputes, chargebacks, or reversals reduced the payout?
Which fees, taxes, or adjustments explain the difference between Shopify sales and PSP payouts?
Which transactions were paid in one period but settled in another?
Which items need follow-up or internal review?

This template is useful for Shopify stores, D2C brands, eCommerce finance teams, online sellers, accounting teams, and companies that need a repeatable Shopify payment reconciliation process.

Required files for this template

Cointab's ready-made workflow is designed around Shopify order records and PSP reports used for payment, refund, fee, dispute, settlement, and payout reconciliation.

Data source	Example records
Shopify Order Report	Used as the internal source-of-truth report containing orders, order IDs, customer details, payment status, gross sales, discounts, taxes, shipping, refunds, and net sales.
PSP Payment Report	Used to compare Shopify orders with payment gateway or PSP transactions, payment IDs, customer references, transaction status, and payment amounts.
PSP Settlement / Payout Report	Used to compare PSP payment activity with settlement-level or payout-level data and final amounts received.
Refund Report	Used where Shopify refunds, PSP refunds, cancellations, returns, or customer credits need to be reconciled separately.
Fee / Adjustment Report	Used where PSP fees, processing charges, taxes, currency conversion, adjustments, or balance movements need to explain payout differences.
Dispute / Chargeback Report	Used where disputes, chargebacks, reversals, or dispute fees need to be reviewed separately or enriched into the workflow.
Bank Statement	Optional, but useful if the finance team also wants to compare PSP payouts with actual bank credits.
Internal ERP / Books Report	Optional, but useful if the finance team wants to compare Shopify and PSP data with accounting, ERP, revenue, receivable, or books records.
Supporting Data	Optional supporting files can be used for SKU mapping, customer mapping, order mapping, payment method mapping, tax logic, currency conversion, store mapping, or other enrichment.

What Cointab matches in Shopify PSP reconciliation

Cointab compares Shopify orders, PSP payments, refunds, fees, disputes, settlements, payouts, and bank receipts across internal and external reports.

Shopify orders and PSP payments

Match Shopify orders, order IDs, or payment references with corresponding PSP payment transactions.

Refunds and cancellations

Identify whether Shopify refunds, cancellations, returns, and customer credits are correctly reflected in PSP records.

Fees and deductions

Track PSP processing fees, transaction charges, dispute fees, taxes, currency conversion differences, and other deductions where available.

Disputes and chargebacks

Review disputed payments, chargebacks, reversals, claims, and related adjustments that affect net payout.

Settlement and payout amounts

Compare expected Shopify payment collections with actual PSP settlement or payout records.

Bank and books records, if added

If bank statements, ERP, or books data are included, Cointab can also compare PSP payout records against bank credits and accounting entries.

Common Shopify PSP reconciliation exceptions

Cointab helps finance teams focus on differences instead of manually reviewing every Shopify order and PSP transaction.

Shopify order not found in PSP

A Shopify order appears in the order report but is not found in the PSP payment report for the selected period.

PSP payment without matching Shopify order

A PSP payment appears without a clear matching Shopify order, invoice, customer, or internal sales record.

Amount mismatch

The order or payment reference matches, but the Shopify order amount and PSP payment amount are different.

Refund difference

A refund appears in Shopify or the PSP report but does not match the expected refund, return, cancellation, or customer credit record.

Fee or deduction difference

PSP fees, processing charges, dispute fees, taxes, currency conversion, or adjustments explain part of the difference between gross sales and net payout.

Settlement timing difference

A Shopify payment belongs to one period but is settled or paid out in a later PSP settlement cycle.

Dispute or chargeback difference

A disputed transaction, chargeback, reversal, or dispute fee affects the payout but is not clearly reflected in Shopify or internal records.

Bank receipt mismatch

The PSP payout amount does not match the amount received in the bank statement.

Duplicate or repeated entry

The same Shopify order, PSP payment, refund, dispute, or payout entry appears more than once or is included in multiple files.

Missing or unclear reference

Shopify order ID, payment ID, transaction ID, customer reference, payout ID, or bank reference is missing, incomplete, or appears inside a description field.

Skipped record

A row cannot be reconciled because required data is missing, invalid, duplicate, incomplete, or unusable.

How this ready-made reconciliation works

Cointab pre-configures the workflow so your team does not need to rebuild the Shopify PSP reconciliation setup every period.

Select the template

Choose Shopify vs PSP from popular reconciliations.

Select the period

Choose the day, week, month, quarter, year, lifetime period, or custom period you want to reconcile.

Upload Shopify and PSP reports

Upload your Shopify order report, PSP payment report, and any required refund, fee, dispute, settlement, payout, bank, or supporting files.

Validate file format

Cointab checks whether the uploaded files match the expected structure and highlights missing or incorrect columns.

Run reconciliation

Cointab applies predefined data preparation and matching logic for Shopify and PSP data.

Review output

View fully matched, partially matched, unmatched, and skipped records.

Download or automate

Download the Excel report, or automate future data input and output through email, SFTP, or APIs.

Structured matching first, AI assistance for difficult cases

Cointab applies structured reconciliation logic first, then uses AI to help with difficult open transactions where fixed rules are not enough.

Structured matching

Structured matching can use:

Shopify Order IDOrder numberInvoice numberCustomer IDCustomer emailPayment IDPSP Transaction IDPSP Charge IDSettlement IDPayout IDRefund IDDispute IDBank referencePayment methodAmount fieldsFee fieldsTax fieldsCurrency fieldsDate fieldsDerived or cleaned identifiers

Matching scenarios

One-to-one
One Shopify order matches one PSP payment.
One-to-many
One Shopify order maps to multiple PSP records such as payment, fee, refund, adjustment, dispute, or payout entries.
Many-to-one
Multiple Shopify orders or PSP payments are grouped into one settlement, payout, or bank deposit.
Many-to-many
Multiple Shopify records and multiple PSP records are grouped and compared.
Partial matching
Identifiers match, but amounts differ.
Net and contra matching
Sales, refunds, disputes, fees, taxes, adjustments, currency conversions, and payouts are netted where required.

AI-assisted transaction matching

After structured rules run, AI helps match difficult open transactions where:

References are incomplete
Shopify and PSP references do not match directly
Descriptions contain embedded order, customer, payment, or payout references
Refund or dispute entries do not directly map to sales
Amounts require contextual understanding
Payment and settlement dates fall in different periods
Currency conversion creates amount differences
Multiple possible matches exist

AI exception analysis

For transactions that remain open, AI can help identify possible reasons such as:

Settlement timing differenceMissing PSP reportRefund adjustmentDispute or chargebackFee or deduction differenceCurrency conversion differenceBank receipt mismatchDuplicate entryInternal Shopify data issueIncorrect payment statusMissing order or payment reference

AI assists matching and exception review, but Cointab keeps reconciliation transparent, reviewable, and audit-friendly.

Audit-ready Shopify PSP reconciliation reports

Cointab gives your team a clear report showing which Shopify and PSP transactions matched, partially matched, remained unmatched, or were skipped.

Report categories

Fully matched
Shopify and PSP records where identifiers and amounts match.
Partially matched
Records where identifiers match but amounts differ.
Unmatched in Shopify
PSP payments, refunds, fees, disputes, settlements, or payouts that do not clearly match Shopify orders.
Unmatched in PSP
Shopify orders, refunds, or internal sales records that are not found in PSP reports.
Skipped
Records excluded due to missing, invalid, duplicate, incomplete, or unusable data.

Report capabilities

Summary cards
Transaction-level details
Filters for review
Payment-method view
Payout-level view
Difference amounts
Matched transaction drill-down
Manual match
Undo manual match
Excel export
Audit-friendly output

Automate recurring Shopify PSP reconciliation

Once this workflow is stable, Cointab can automate file input, reconciliation runs, and output delivery.

Bring data into Cointab

Data can be received or pulled through:

EmailSFTPAPI integrations, where available

Run automatically

Schedule reconciliation:

DailyWeeklyMonthlyEnd of dayAfter file receiptAfter all required files are availableAt a custom frequency

Push output back

Send reconciliation output to:

ERPAccounting systemBI dashboardInternal finance systemAnalytics databaseData warehouseInternal exception trackereCommerce operations system

Matched Shopify orders
Matched PSP payments
Unmatched Shopify records
Unmatched PSP records
Refund differences
Dispute or chargeback differences
Fee or deduction differences
Currency conversion differences
Payout differences
Bank receipt differences
Open items
Suggested actions
Excel reconciliation report
Structured API output

View a Shopify PSP reconciliation demo report

See how Cointab presents Shopify vs PSP output with matched, partially matched, unmatched, and skipped transactions.

Shopify vs PSP Demo

Explore a sample report showing Shopify orders, PSP payments, refunds, fees, disputes, settlements, payouts, bank receipts, and open items.

View demo report

Explore related payment gateway and eCommerce reconciliations

Cointab supports other eCommerce, PSP, payment gateway, settlement, and payout reconciliation workflows.

Sales vs Payment Gateway

Use a general payment gateway reconciliation workflow for sales, payments, refunds, fees, and settlements.

View template

Sales vs Stripe

Reconcile internal sales with Stripe payments, refunds, settlements, fees, disputes, and payouts.

View template

Sales vs PayPal

Match internal sales or order records with PayPal payments, refunds, fees, disputes, and payouts.

View template

Sales vs PG vs Bank

Match sales with payment gateway records and final bank credits.

View template

Built for Shopify stores and teams reconciling PSP payments

This template is useful for teams that regularly reconcile Shopify orders, PSP payments, refunds, fees, disputes, settlements, payouts, and bank receipts.

Shopify stores

For businesses using Shopify as their storefront and reconciling orders with PSP payments, refunds, and settlements.

D2C brands

For D2C teams managing high-volume online orders, payment gateway transactions, refunds, and payout differences.

eCommerce finance teams

For teams handling Shopify reports, PSP reports, payout records, bank deposits, and exception review.

Accounting teams

For teams preparing reconciliation reports for month-end close, books, revenue review, receivables, and audit.

Operations teams

For teams that need visibility into order status, payment status, refund status, and unresolved payment exceptions.

Outsourced finance teams

For accounting firms or finance operations teams handling Shopify and PSP reconciliation for multiple clients.

Trusted by teams handling eCommerce and payment reconciliation

Cointab is used by finance and operations teams that reconcile high-volume, multi-source transaction data across eCommerce platforms, payment gateways, marketplaces, banks, partners, and internal systems.

“We have worked on many softwares but we love the ease of using cointab. The staff and support is very instant. They are approachable, proficient and patient. Team is very cooperative with the customisations. The experience of using cointab was nice.”
— Urbanic

Shopify vs PSP FAQs

Start Shopify vs PSP reconciliation

Use Cointab's ready-made Shopify PSP reconciliation workflow to match orders with payments, identify payout differences, review exceptions, and export audit-ready reports.

Start this reconciliation Schedule guided setup

View demo report

Ready-made workflow · Reusable every period · Manual upload and automation supported

Shopify vs PSP Reconciliation

Reconcile Shopify orders with PSP payments, refunds, fees, disputes, settlements, and payout reports in one structured workflow.

Upload your Shopify and PSP reports, select the period, run reconciliation, and review fully matched, partially matched, unmatched, and skipped records.

View demo report

Ready-made workflow · Reusable every period · Manual upload or automated data flow

Data source

Example records

Shopify Order Report

Used as the internal source-of-truth report containing orders, order IDs, customer details, payment status, gross sales, discounts, taxes, shipping, refunds, and net sales.

PSP Payment Report

Used to compare Shopify orders with payment gateway or PSP transactions, payment IDs, customer references, transaction status, and payment amounts.

PSP Settlement / Payout Report

Used to compare PSP payment activity with settlement-level or payout-level data and final amounts received.

Refund Report

Used where Shopify refunds, PSP refunds, cancellations, returns, or customer credits need to be reconciled separately.

Fee / Adjustment Report

Used where PSP fees, processing charges, taxes, currency conversion, adjustments, or balance movements need to explain payout differences.

Dispute / Chargeback Report

Used where disputes, chargebacks, reversals, or dispute fees need to be reviewed separately or enriched into the workflow.

Bank Statement

Optional, but useful if the finance team also wants to compare PSP payouts with actual bank credits.

Internal ERP / Books Report

Optional, but useful if the finance team wants to compare Shopify and PSP data with accounting, ERP, revenue, receivable, or books records.

Supporting Data

Optional supporting files can be used for SKU mapping, customer mapping, order mapping, payment method mapping, tax logic, currency conversion, store mapping, or other enrichment.

Start Shopify vs PSP reconciliation

Use Cointab's ready-made Shopify PSP reconciliation workflow to match orders with payments, identify payout differences, review exceptions, and export audit-ready reports.

View demo report

Ready-made workflow · Reusable every period · Manual upload and automation supported