The Hidden Challenge of Manual Reconciliation in Payments—and Why Automation Is the Future


By Aaron Holmes, CEO of Kani Payments

The payments industry moves fast. Billions of transactions flow through every day, across systems, currencies and payment channels. But behind the slick front-end experience lies a complex, manual reconciliation process that many financial institutions are still trying to manage with spreadsheets. As transaction volumes surge and regulatory demands grow, those old methods just aren’t holding up.

At Kani, we’ve been digging into the state of reconciliation and reporting across the industry. Our 2025 Payments & Reconciliation Survey gathered insights from 250 UK-based issuers, acquirers, processors, neobanks and e-money institutions to understand the day-to-day challenges firms are facing behind the scenes.

The findings were clear: inefficiencies in reconciliation and reporting are eating up time, draining resources and putting compliance at risk. Automation is no longer a luxury; it’s becoming essential.

The Spreadsheet Struggle

Reconciliation tasks are consistently flagged as one of the biggest operational burdens in payments. Teams are bogged down in manual data collection, exception handling and cross-checking reports. Our research found that firms are losing over 700 hours a year just on data preparation, and 82% struggle to deliver reports on time.

The root cause? More than half (56%) of payments companies are still relying on spreadsheets. Among those, 94% frequently miss reporting deadlines, and 71% say building reports is unnecessarily time-consuming. These numbers tell a clear story: manual tools aren’t keeping up with modern payment complexity.

Worse still, 53% of professionals say too much of their bandwidth is tied up in reporting tasks. That’s time that could be spent driving growth, improving controls or solving strategic problems.

What’s making reconciliation harder? Scale. Cross-currency transactions, multiple payment channels and high volumes were the top barriers to accurate matching. That complexity leads to mismatches, which then creates the need for time-consuming exception management, a pain point for 1 in 3 firms.

The Gradual Shift Toward Automation

We’re seeing signs of change. The industry is slowly shifting from manual-heavy processes to more automated models. Nearly seven in ten (68%) firms are using either partially or fully automated systems to handle reconciliation and reporting.

But partial automation only gets you so far. To meet the demands of modern finance, payments companies need end-to-end automation, from data ingestion and standardisation to reporting, validation and delivery.

The Real Cost of Errors

Reconciliation errors don’t exist in a vacuum—they cascade through the business. The cost isn’t just time lost fixing issues. It’s the compounding risk to data integrity, auditability and business confidence.

When we asked firms about their top concerns, 35% pointed to financial discrepancies, and 34% said reconciliation issues had a direct impact on investment or growth decisions. That’s a red flag. These aren’t just operational delays—they’re symptoms of deeper data quality issues that can undermine trust and distort decision-making.

Compliance Under Pressure

Whether it’s quarterly scheme reports, period-end close or regulatory returns, compliance reporting is always a race against the clock. With complex data flows and fragmented systems, 82% of firms told us they struggle to meet deadlines. And for those relying solely on spreadsheets, that figure rises to 94%.

The risk is more than missing deadlines—it’s compromising the quality of submissions, losing audit trail visibility and triggering downstream issues across finance, compliance and risk teams. After all, compliance is about credibility as much as it is about submitting the numbers.

The Future Is Frictionless

Manual reconciliation won’t survive the next wave of growth and regulation. As AI, embedded finance and real-time payments scale, firms won’t be able to keep pace with spreadsheets and legacy workarounds.

The future belongs to firms that put automated, auditable infrastructure at the heart of their finance operations. That means reducing manual touchpoints, increasing visibility and ensuring reporting is built on trusted data.

The result? Fewer errors. Stronger compliance. More time for teams to focus on strategic work, not firefighting spreadsheets.

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