In today’s high-volume, multi-channel payments environment, choosing the right payment reconciliation software is as much a strategic decision as it is a technical one. Yet many businesses are still battling through spreadsheets, semi-automated workarounds and home-grown scripts that can’t scale.
As payment complexity grows, so too does the risk of mismatches, reporting delays and regulatory pressure. Businesses need an end-to-end solution that’s purpose built for the challenges of payment reconciliation, like fragmented data, complex transaction flows and mounting compliance demands.
We analysed insights from Kani’s Payment Reconciliation & Reporting Survey 2025—capturing feedback from over 250 UK payments firms—to help you identify what really matters when choosing a solution.
✅ 1. Automated, scalable data ingestion
Why it matters: 47% of survey respondents cited fragmented data as their top barrier to accurate reconciliation and reporting. That’s because each payment provider—whether processor, bank, card scheme or PSP—delivers data in its own structure, using different naming conventions, file formats, encoding standards and metadata assumptions.
Files arrive as CSVs, PDFs, ISO20022 XMLs or API payloads—often with missing fields, inconsistent delimiters and undocumented schema changes. The bottleneck presented by inconsistent data is no joke: the average UK payments businesses spends 3 hours preparing data before reconciliation can even begin. Assuming daily reconciliation, this equates to a staggering 700 hours annually.
What to look for
To overcome this, your software should support ingestion that’s
- Format-agnostic, able to ingest files via SFTP, API or drag-and-drop uploads
- Schema-flexible, allowing non-technical teams to map and align fields without scripting
- Intelligent, with automated file classification, header detection and validation on upload
- Built for scale, able to process large, multi-source datasets concurrently
Without scalable ingestion, you’re not automating reconciliation—you’re just moving the manual effort upstream.
✅ 2. Built-in data standardisation and error handling
Why it matters: Matching logic relies on consistent semantics. But real-world payment data often arrives with local timestamp formats, inconsistent currency rounding, merged values (e.g. “2025-03-01 EUR 10.00”) or shifted columns due to upstream file edits.
Without robust standardisation and pre-matching validation, errors are simply carried into the reconciliation stage—where they cause false mismatches, audit trail breaks and duplicate exceptions.
53% of firms say too much time is spent formatting reports rather than fixing actual problems. That’s a sign of systemic inefficiency: time spent wrangling format issues instead of addressing root-cause data integrity.
What to look for
Obtaining clean, standardised data requires software with built-in:
- Timezone conversion and ISO 8601 formatting
- Normalisation of currency and amount fields, including FX rates and decimal rounding
- Parsing of embedded metadata fields
- Auto-validation of required fields, column counts and row-level integrity
Effective reconciliation software should act like a compiler, catching data issues early before they corrupt downstream logic.
✅ 3. Multi-layered reconciliation logic
Why it matters: Payments don’t follow neat one-to-one patterns. You might reconcile an authorisation against multiple settlements, account for a partial refund or trace a processor deposit to multiple ledger entries (each with FX conversion and fee offsets).
Our research shows that 23% of firms struggle with FX matching, and 20% face daily issues with chargebacks and reversals. Yet many reconciliation tools are built on simplistic matching engines that assume static, one-to-one relationships.
Modern software must accommodate real payment flows: chained events, many-to-many mappings, value tolerances, time-based matching and rolling cut-off rules.
What to look for
To reconcile modern payment flows, software should enable:
- Configurable, rules-based matching (e.g. tolerance bands, date windows, chained matching)
- FX-aware matching, including rate source tracking and rounding logic
- One-to-many and many-to-one relationship support
- Sub-ledger and multi-layer reconciliation (e.g., PSP → processor → bank)
- Time-sequenced logic for event-driven workflows (e.g., authorisation → settlement → refund → dispute)
The real test of payment reconciliation software isn’t how it handles perfect data—it’s how it handles edge cases without falling apart.
✅ 4. Exception management that’s audit-ready
Why it matters: Exception handling is where teams lose visibility. When unmatched transactions spill into offline spreadsheets or Slack threads, the audit trail breaks. Regulators don’t just care that issues are resolved—they care that resolution is traceable, timely and documented.
Kani’s survey found that 82% of payments firms have missed a reporting deadline due to delays or inconsistencies in reconciliation. And with growing regulatory scrutiny, ad-hoc exception handling is no longer acceptable.
Exception workflows must be centralised, rule-driven and logged end-to-end.
What to look for
Managing exceptions effectively requires software that can:
- Automatically triage breaks into queues based on rule logic or exception type
- Assign owners, track resolution notes and log time-stamped user actions
- Escalate unresolved items before deadlines are missed
- Export clean audit packs with full history of edits, comments and status changes
Good reconciliation software builds defensible, regulator-friendly audit trails you don’t have to assemble manually.
✅ 5. End-to-end reporting and compliance outputs
Why it matters: Reporting is where the value of reconciliation becomes tangible. Whether it’s safeguarding submissions to the FCA or Mastercard QMR and Visa GOC files, the ability to generate clean, compliant reports instantly can make or break your operations.
Yet even fully automated systems are struggling: 60% of firms using them say reporting still takes too long. That’s often due to misconfigured templates, poor source data linkage or rigid output formats that don’t match evolving requirements.
Your reconciliation software should be your reporting engine—not a pre-step to another manual process.
What to look for
To make reporting seamless, aim for software that includes:
- Pre-built templates for FCA, card scheme and regulatory outputs
- User role-based sign-off workflows and approval logs
- Field locking to prevent post-submission edits or accidental change
- Secure access links for auditors and external stakeholders
- Time-stamped submission logs and secure access links for regulators
When reconciliation software closes the loop between data, resolution and reporting, deadlines stop being a source of stress and instead become a source of confidence.
Final thoughts: Your checklist is your strategy
Choosing payment reconciliation software is ultimately about choosing control: over data, processes, compliance and operational scale.
From ingestion to exception handling, the right platform transforms reconciliation from a firefighting task to a strategic capability. If your team is spending more time collecting, formatting or investigating than analysing and reporting, it’s time to upgrade.
📊 Want to learn more? Explore how Kani helps automate reconciliation workflows end-to-end—from ingestion to audit.
FAQs
What is payment reconciliation software and how does it work?
Payment reconciliation software automates the process of matching internal financial records—like ledger entries or ERP data—with external sources such as bank statements, card scheme reports and PSP files. Unlike basic tools, advanced solutions can ingest data from multiple formats (CSV, JSON, XML), apply layered matching logic (including FX handling and partial settlements) and flag exceptions in real time. This eliminates the manual overhead of spreadsheets and reduces risk from errors, delays and fragmented audit trails.
What features should you look for in payment reconciliation software?
The best payment reconciliation software should go beyond simple transaction matching. Key features include: automated data ingestion from multiple sources, configurable matching logic to handle many-to-many relationships and FX variances, rule-based exception management, built-in regulatory reporting templates (e.g. FCA, Mastercard QMR) and secure audit logs. Scalability and ease of integration with existing systems (like ERPs, processors, or bank feeds) are also critical for long-term success.
How does payment reconciliation software reduce errors?
Payment reconciliation software reduces errors by enforcing data validation and standardisation before matching occurs. It can automatically detect missing fields, formatting mismatches, duplicate entries or out-of-tolerance variances that would otherwise go unnoticed. According to the Kani Reconciliation & Reporting Survey 2025, 44% of reconciliation errors are due to manual work and poor integration—issues that automation directly mitigates.
Can payment reconciliation software handle cross-currency and multi-channel payments?
Yes, modern payment reconciliation software is designed to handle the complexity of multi-currency, multi-channel payment flows. It supports FX-aware matching, fee offsets and chained reconciliations (e.g., PSP → processor → bank), using tolerance rules and timestamp logic to account for time lags and currency conversions. This is essential for high-growth payment businesses dealing with international operations and varied settlement timelines.
What types of businesses need payment reconciliation software?
Any business processing large volumes of payments—particularly across multiple providers, currencies or regions—can benefit from payment reconciliation software. This includes payment processors, e-money institutions, card issuers and acquirers, neobanks and fintechs. Automated software helps these firms streamline operations, meet reporting obligations and scale without increasing compliance or error risk.
How does payment reconciliation software support compliance and audit readiness?
Payment reconciliation software supports compliance by generating regulatory-ready reports and maintaining a full audit trail of user actions, data edits and exception resolutions. Many platforms offer templates for FCA safeguarding, Mastercard QMR, and scheme-specific reporting. By automating workflows and locking post-submission data, these tools ensure accuracy, consistency and transparency—critical for passing audits and meeting submission deadlines under scrutiny.
What are the problems with payment reconciliation?
Payment reconciliation presents several recurring challenges—especially as payment volumes, partners, and formats increase. Key problems include data fragmentation, manual intervention, complex transaction flows, timing mismatches, limited auditability and compliance pressures.
