Microsoft Dynamics NAV Payment Gateway Reconciliation

Cointab helps finance teams reconcile Microsoft Dynamics NAV exports with payment gateway reports in a structured, auditable workflow. Instead of comparing files manually in Excel, users can upload both sides of the data, map the required fields once, run reconciliation, and review matched, partially matched, unmatched, and skipped transactions in one report.

This is useful when the business wants to compare expected receipts recorded in Microsoft Dynamics NAV with the settlement or transaction data received from payment gateways. It helps teams identify timing differences, missing settlements, underpayments, refunds, fees, chargebacks, duplicate entries, and other exceptions that can affect books and month-end close.

Why reconcile Microsoft Dynamics NAV with payment gateway reports

Microsoft Dynamics NAV often acts as the internal record for invoices, receivables, sales, or ledger entries. Payment gateway reports show what was processed, settled, reversed, refunded, or withheld by the external provider. Finance teams need both sides to agree, or at least understand why they do not.

Manual reconciliation becomes difficult when:

• transaction volumes are high
• multiple gateways are involved
• settlement files use different identifiers
• fees and deductions need to be netted out
• refunds or partial payments create amount differences
• the same workflow must be repeated every period

Cointab makes this process reusable. Once the workflow is set up, the team can reconcile future periods with the same configuration instead of rebuilding formulas and lookups every time.

What data goes on each side

Cointab uses a Side A and Side B model so finance teams can clearly define what is being compared.

Side A: Microsoft Dynamics NAV records

Side A contains the records the business expects to be correct. For this workflow, that usually includes exports from Microsoft Dynamics NAV such as:

• sales or invoice reports
• receivables or ledger data
• order-level internal records
• ERP exports with dates, amounts, and identifiers

Side B: payment gateway records

Side B contains the records received from the external source. For this workflow, that usually includes:

• payment gateway transaction reports
• settlement reports
• payout reports
• refund or reversal files
• fee and deduction details

Users can upload CSV, XLS, or XLSX files and configure the required columns such as date, amount, and reference fields like order ID, transaction ID, invoice number, or settlement reference.

How the reconciliation workflow works

A typical reconciliation setup follows a simple sequence:

1. Upload the Microsoft Dynamics NAV export on Side A.
2. Upload the payment gateway report on Side B.
3. Map the key fields such as date, amount, and identifiers.
4. Optionally add supporting data for lookup, enrichment, or merging.
5. Create derived columns if a field needs cleaning or calculation.
6. Run reconciliation manually or on a schedule.
7. Review the reconciliation report and exception buckets.
8. Download the Excel report for internal review or audit support.

If a required file arrives late, users can upload the missed file under the same reconciliation and refresh the report.

Common reconciliation outcomes

Cointab separates records into clear buckets so finance teams can focus on exceptions instead of reviewing everything manually.

Fully matched

These are transactions where the identifiers and amounts match according to the configured rules. For example, an invoice or order in Microsoft Dynamics NAV matches a gateway transaction and settlement amount.

Partially matched

These are transactions where the identifiers point to the same business event, but the amounts do not match exactly. This may happen because of fees, deductions, refunds, partial capture, or settlement differences.

Unmatched

These are records present on one side but not found on the other. Examples include:

• a payment recorded in Microsoft Dynamics NAV but missing in the gateway report
• a gateway transaction present in the settlement file but not posted in NAV
• a refund or reversal that does not have a matching internal entry

Skipped

These are rows that were not included in reconciliation because of issues such as missing fields, invalid amounts, duplicate rows, or file-format problems. Skipped records remain visible so the user understands what was ignored and why.

Where supporting data and derived columns help

Reconciliation often requires more than one primary file. Cointab also supports supporting data on either side for enrichment and preparation.

Examples include:

• product master data
• order metadata
• fee or tax rate files
• mapping sheets
• customer or vendor masters
• return or adjustment reports

Users can also create derived columns from existing data. For example, they can normalize a transaction reference, calculate a net amount, or use AI to generate an Excel-style formula from plain language instructions. That makes it easier to prepare Microsoft Dynamics NAV exports and gateway data for matching.

Matching logic for finance teams

Cointab uses structured matching logic to compare records across the two sides. The engine supports common reconciliation patterns such as:

• one-to-one matching
• one-to-many matching
• many-to-one matching
• many-to-many grouping
• net-to-net comparison
• partial matching
• contra-style matching

It also supports different comparison methods, including equals, contains, similar, and subset-based logic. This is important when transaction references are not identical across systems or when one side splits a payment into multiple records.

After structured matching is complete, AI can help analyze the remaining open items. The goal is to support review, not to force weak matches. If the evidence is not strong enough, the record should stay unmatched.

Why this workflow is useful in monthly close

For finance teams, Microsoft Dynamics NAV reconciliation with payment gateway data is not only about finding differences. It also supports:

• cleaner books and ledger control
• faster exception review
• easier dispute follow-up
• clearer settlement visibility
• better audit readiness
• less spreadsheet dependency

Instead of tracing discrepancies manually across multiple files, teams can view the report dashboard, drill into open items, and understand which records matched, which did not, and what needs attention.

Automation for recurring reconciliations

Once the workflow is configured, Cointab can support recurring reconciliation without repeated manual uploads. Data can be received or pulled through email, SFTP, or API, depending on the setup.

That makes it practical for finance operations that run daily, weekly, or monthly reconciliations. The same workflow can be reused for future periods, and the output can be delivered back to internal systems when required.

Reconciliation report and review

After the run is complete, users can review a report that shows:

• total summary
• fully matched summary
• partially matched summary
• unmatched summary
• skipped summary
• transaction-level detail tables
• filters for deeper analysis
• downloadable Excel output

The report stays available in the dashboard for future reference, making it easier to review historical reconciliations and track who ran each period.

Team-based finance operations

Cointab also supports shared workspaces for finance teams. That means controllers, accountants, and reconciliation analysts can work from the same setup instead of passing spreadsheets around by email. Shared access, roles, and audit logs help keep the process controlled and reviewable.

Common use cases for this reconciliation setup

This workflow is useful when Microsoft Dynamics NAV needs to be reconciled against:

• payment gateway settlements
• payout reports
• refund files
• fee and deduction reports
• transaction statements from one or more external processors

It is especially helpful for businesses that need a repeatable, audit-friendly process for transaction matching and payment reconciliation.

FAQ

How does Cointab reconcile Microsoft Dynamics NAV with payment gateways?

Users upload the NAV export and the payment gateway report, map the required fields, and run reconciliation. Cointab then compares the two sides, groups related transactions where needed, and separates matched, partially matched, unmatched, and skipped records.

What fields are usually mapped for this workflow?

Finance teams usually map date, amount, and a reference or identifier field such as order ID, transaction ID, invoice number, settlement reference, or payment reference. Supporting columns can also be added when needed.

Can recurring reconciliations be reused?

Yes. Once the reconciliation setup is configured, it can be reused for future periods. That helps teams avoid rebuilding the same logic every month.

What if a file is missing during reconciliation?

If a file arrives later, it can be uploaded under the same reconciliation and the report can be refreshed. This is useful when gateway or settlement files are received after the initial run.

Does Cointab only work for payment gateway reconciliation?

No. Cointab is a flexible reconciliation platform for comparing any two sides of financial or operational data, including books vs bank, vendor reconciliation, marketplace settlement reconciliation, and custom internal vs external reports.