Five Warning Signs Your Team is Struggling with Payment Reconciliation

Payment reconciliation may not be headline news, but its impact on financial integrity is significant. Done right, reconciliation catches errors, ensures regulatory compliance and builds trust with customers, partners and oversight bodies.

At its core, payment reconciliation matches transactions across your internal records, bank statements and processor files. It confirms that what should have happened with the money actually did.

Yet, despite its simplicity in theory, real-world reconciliation often turns into a complex nightmare. Global transactions, fragmented data and rapidly evolving regulatory demands mean finance teams frequently find themselves overwhelmed.

So, how can you tell if your team is struggling with payment reconciliation? Here are five warning signs we've observed time and again at Kani.

1. Your Team Spends More Time Prepping Data than Reconciling It

If your team dedicates hours to tracking down missing fields, reformatting processor exports, and enriching incomplete data, your reconciliation process is inefficient and costly.

Our research found UK payment companies spend three hours per day simply gathering, cleaning and formatting data before reconciliation begins. That adds up to 700 wasted hours annually per business. The challenge comes from inconsistent data formats, CSV, ISO20022, PDF, API or bespoke files, varying field names, mismatched time zones and absent metadata.

2. You're Constantly Missing Deadlines

Month-end, quarter-end, scheme reports, audit prep… the deadlines never stop. If your team’s constantly chasing them, something’s off in your process.

And it’s more common than you’d think: 82% of payments companies say they regularly miss reporting deadlines, with that number rising to 94% for spreadsheet users. 

It’s not just the volume of work. 71% also say the reconciliation process takes longer than it should, bogged down by inefficient tools and manual steps. When the process itself is a blocker, something’s got to give.

3. Errors Keep Slipping Through

An error-prone reconciliation process isn’t just inconvenient, it’s dangerous. Mistakes or opaque workflows often lead to delayed/rejected submissions, failed inspections or fines. 

Worse still, subtle issues might go unnoticed until they become critical, putting the entire business at risk. In Kani’s research, 35% of payments companies say reconciliation errors have led to financial discrepancies, while 34% say they’ve directly impacted investment or slowed growth. 

4. Your Team is Stuck in Survival Mode

When reconciliation relies on manual processes, finance teams spend most of their time chasing anomalies, fixing broken formulas and untangling mismatched data. Instead of focusing strategically, they're stuck putting out fires.

This reactive mode drains resources, creates frustration and holds your business back from growth opportunities.

5. You Don’t Trust Your Data

Effective reconciliation depends on quality data. But in payments, data is notoriously fragmented, inconsistent and constantly changing. Problems at the data’s source quietly cascade into larger issues across compliance, reporting, customer service and decision-making.

Failed audits, missed reporting deadlines and inaccurate forecasts are often symptoms of poor data quality, not flawed processes. That’s why we created the Kani Data Scorecard, a diagnostic tool that assesses the quality, completeness and consistency of your payments data across reconciliation, compliance and reporting requirements. It gives businesses a clear, objective view of how their data is performing, what’s missing or misaligned and where improvements are needed.

Whether you're a fintech startup or a global payments provider, fixing the data at its source is the fastest way to improve everything from audits and analytics to customer trust.

A Smarter Way to Manage Payments Data

If any of these signs sound familiar, it’s worth stepping back and reassessing your reconciliation setup. What once worked at a smaller scale may no longer be fit for purpose.

As payment volumes grow and data sources multiply, reconciliation needs to evolve from a manual, reactive task into a structured, repeatable process that’s resilient under pressure. That means aiming for systems that provide full visibility across the transaction lifecycle, from authorisation to settlement, across multiple providers, currencies and formats.

The goal isn’t automation for its own sake, nor is it about replacing people. It's about giving teams the tools to spot issues early, close the books faster and trust the numbers. The right setup will deliver clarity, consistency and control, freeing finance teams to focus on what moves the business forward.