How to Solve the 7 Biggest NetSuite Reconciliation Challenges

If you’ve spent hours wrestling with reconciliation in NetSuite, you’re not alone.

Manual effort, inconsistent imported bank data, and high transaction volumes make it harder than it should be. And when finance teams can’t reconcile accounts efficiently, the entire financial close process suffers. The key is knowing where the roadblocks lie—and how to move past them.

This article breaks down the seven biggest reconciliation challenges in NetSuite and shares best practices for solving them.

Challenge 1: High Transaction Volumes

As transaction volumes grow, so does the complexity of reconciliation in NetSuite. Finance teams handling thousands of general ledger transactions, bank transactions, and account transactions quickly run into reconciliation bottlenecks. The reconciliation process becomes slow, errors creep in, and the financial close process drags on.

NetSuite’s native tools help, but they often require manual intervention when imported bank data doesn’t line up perfectly. That means finance teams spend hours trying to match transactions one by one—time that could be spent on higher-value financial management activities.

This is where Kolleno can help.

By integrating directly with NetSuite, Kolleno’s payment reconciliation applies intelligent transaction matching to high volumes of bank data, automatically linking journal entries, payments, and bank statements. Finance teams can create custom rules, reduce unmatched transactions, and automate reconciliation across multiple accounts. This leads to fewer errors and a more streamlined reconciliation process.

Challenge 2: Data Discrepancies from Imported Bank Data

Imported bank data doesn’t always play nicely with NetSuite. Formatting errors, excluded transactions, or delays in imported bank transactions often lead to mismatches. When bank statements and general ledger transactions don’t align, finance teams are left chasing discrepancies instead of moving the financial close forward.

NetSuite offers the match bank data page, which helps finance teams review imported bank data and reconcile transactions against the GL. But even with this tool, high-volume accounts often generate unmatched transactions that require time-consuming manual intervention.

Kolleno helps solve this challenge by cleaning and structuring bank data before it ever hits NetSuite. With intelligent transaction matching, Kolleno automatically flags discrepancies, reconciles account statement pages, and reduces the number of unmatched transactions finance teams need to review manually.

This leads to clearer bank reconciliation and faster closes, while also giving teams more confidence in their financial reporting.

Challenge 3: Manual Reconciliation and Human Errors

Manual reconciliation is one of the biggest drains on finance teams. Every time transactions are keyed in by hand, the risk of data entry mistakes, duplicate payments, or mismatched transactions grows. The more accounts and bank statements involved, the harder it becomes to maintain accurate financial records.

NetSuite’s native tools reduce some of this burden, but finance teams still spend valuable hours reconciling accounts line by line. In a high-volume environment, that manual effort slows down the financial close process and undermines financial accuracy.

Kolleno removes much of this risk by automating reconciliation in NetSuite. Its intelligent transaction matching reduces the need for manual intervention, while custom rules ensure recurring transactions match automatically.

Challenge 4: Timing Differences and Outstanding Transactions

Even when the reconciliation process runs smoothly, timing differences create unavoidable gaps. Outstanding transactions—like checks that haven’t cleared, card payments still in transit, or bank fees that haven’t been posted—cause temporary mismatches between NetSuite’s general ledger and external bank statements. These discrepancies make it harder for finance teams to track cash balances and keep cash flow reporting accurate.

NetSuite’s reconcile account statement pages and reconciliation status tracking help identify these issues, but resolving them often requires manual monitoring and exception handling. For finance teams working under pressure during the financial close process, these delays can quickly add up.

Kolleno helps by surfacing these discrepancies in real time. Its integration with NetSuite automatically flags unmatched transactions and outstanding items, ensuring they’re clearly marked for review. Finance teams can reconcile transactions faster, maintain accurate financial records, and keep cash flow visibility intact—even when timing differences occur.

Challenge 5: Multi-Entity and Intercompany Reconciliations

For growing businesses, reconciling accounts across multiple subsidiaries or related entities is one of the toughest parts of financial management. Intercompany reconciliations involve high transaction volumes, multiple bank accounts, and complex general ledger structures. Without a clear process, finance teams face reconciliation bottlenecks, mismatched transactions, and delays in consolidating balance sheet accounts.

NetSuite ERP offers tools for managing intercompany reconciliations. However, the process can still feel heavy when manual intervention is required. Finance teams must reconcile transactions between entities, check reconciliation history, and ensure balance sheet accounts line up—while also preparing for regulatory compliance and audit readiness.

Kolleno simplifies this complexity by centralizing reconciliation activities. Its integration with NetSuite gives finance teams real-time visibility across entities, enabling them to match transactions consistently and maintain accurate financial records across all accounts.

Challenge 6: Compliance, Audit, and Internal Controls

Strong reconciliation practices aren’t just about closing the books. They’re about protecting financial accuracy, meeting regulatory compliance standards, and being ready for audits at any time.

NetSuite does provide some tools to help finance teams strengthen their reconciliation process. Unfortunately, in practice, gaps remain. Manual reconciliation activities, incomplete audit trails, and inconsistent exception handling create weak spots that can delay the financial close process and increase risk.

Kolleno strengthens this layer of control. By automating reconciliation in NetSuite, Kolleno ensures every matched transaction leaves a clear audit trail. Finance teams gain full visibility into reconciliation status across accounts, maintain accurate financial records, and meet compliance requirements with less manual effort.

The result? Better audit readiness and greater confidence in financial reporting.

Challenge 7: Limited Visibility in NetSuite’s Native Tools

NetSuite’s native reconciliation tools are powerful, but they don’t always give finance teams the real-time visibility they need. Tracking reconciliation status across multiple bank accounts, balance sheet accounts, and high-volume transactions can feel like working in the dark. Without clear dashboards and streamlined reconciliation process workflows, discrepancies often go unnoticed until the financial close process is already delayed.

While the match bank data page and reconcile account statement pages help match transactions against imported bank data, visibility gaps remain. Finance teams can struggle to see which transactions are reconciled and which remain unmatched. Worst of all, they can’t identify where manual intervention is needed. That slows down decision making and undermines financial management.

Kolleno helps bridge this gap. Its integration with NetSuite gives finance teams real-time visibility into account reconciliation activities across entities and accounts. By highlighting unmatched transactions, surfacing discrepancies, and automating exception handling, Kolleno turns reconciliation from a reactive task into a proactive, continuous process.

Final Thoughts

NetSuite users face seven major challenges when it comes to reconciliation. Thankfully, they can all be solved. By applying the best practices outlined above, finance teams can move past these reconciliation challenges and focus on strategic financial management.

That’s where Kolleno comes in. As a NetSuite partner, Kolleno helps finance teams automate reconciliation, reduce discrepancies, and maintain accurate financial records across accounts and entities. Put simply, it turns reconciliation from a time-consuming task into a streamlined process.

Ready to see how it works? Book a demo with Kolleno and discover how to simplify NetSuite account reconciliation.