3 Common AP Automation Challenges (And Their Solutions)

Accounts payable (AP) automation has become an essential tool for modern finance teams. By replacing manual AP processes with automated solutions, organizations aim to gain cost savings, efficiency, and real-time visibility across financial processes.

 

However, many businesses encounter recurring AP automation challenges that prevent them from realizing the full value of their investments. We’ve compiled a list of the top automation issues our clients face in their AP departments. Let’s take a look at the accounts payable automation solutions that are most effective at addressing them.

AP Automation Challenge 1: Automating Inefficient Processes

The first mistake organizations make is trying to automate broken processes. Too often, AP teams rush to deploy software without asking if the underlying workflows even make sense. That means bottlenecks, outdated approval chains, or redundant steps don’t disappear; they just happen more quickly.

 

Chuck Hagood, Executive Vice President at Illumis Global, put it best: “People often think that automation and technology will automatically make things better. But if you’re not careful, it can just make things faster. You make the same mistakes you’ve always made; you just do it at a more rapid pace.

How Automating Inefficient Processes Can Impact Your AP Operations

  • Speed Without Quality: An inefficient process run by a machine is simply an inefficient process at scale. Automating these processes can make errors occur more quickly and in higher volume, compounding their impact on AP operations.
  • Hidden Costs: Instead of achieving cost savings, finance teams often find themselves spending more to resolve downstream errors. Detecting duplicate payments, reconciling mismatched invoice data, and fielding supplier disputes all create extra work and added expense.
  • Reduced Trust: Once stakeholders lose faith in the accuracy of automated solutions, adoption falters. The resulting resistance can hinder automation initiatives and undermine the long-term value of the investment.

AP Automation Solutions for Efficient Processes

  • Map Your Workflows Before Implementing AP Automation. Document each step and identify bottlenecks such as manual AP procedures, missing approval controls, or outdated payment processes. This helps ensure that your automation works for you, not against you.
  • Run an Accounts Payable Recovery Audit First. In addition to recovering profits, accounts payable recovery audits can identify areas to improve in your processes. They can be a powerful tool to help you set up your AP automation for success. 
  • Optimize, Then Automate. Technology should reinforce best practices, not copy bad habits. Address approval chains, exception routing, and vendor communication gaps before introducing automated solutions.
  • Utilize Business Intelligence Solutions. Business intelligence tools like IBIS™ allow AP teams to analyze patterns in invoice processing and find areas to improve. This helps prevent recurring issues in your AP workflow.

AP Automation Challenge 2: Incomplete or Inaccurate Vendor Master Data

Even the best AP automation software can’t function properly without clean, reliable vendor data. And when it comes to automating accounts payable, the vendor master file is often the weakest link.

 

Many companies have duplicate supplier records, outdated payment terms, or missing tax IDs in their vendor database. Once automation kicks in, it only amplifies these issues. The system may choose the wrong vendor record, apply the wrong payment terms, or route invoices incorrectly — all without alerting the user.

How a Disorganized Vendor Master File Can Impact Your Accounts Payable Operations

  • Duplicate Payments: Inaccurate invoice data can lead to costly errors when the same supplier appears under multiple records. These duplicate entries confuse automated systems and make it easier for overpayments to slip through unnoticed.
  • Compliance Risks: Vendor information tied to outdated addresses, tax IDs, or banking details may expose organizations to fraud. It also creates problems during tax season, when inaccurate reporting can trigger penalties or audits.
  • Failed Integrations: When companies consolidate systems or migrate accounting platforms, poor vendor data slows the transition and introduces errors. This not only increases project costs but also disrupts day-to-day AP workflows during the changeover.

Vendor Master Data Management Best Practices for AP Automation

  • Prioritize a Vendor Master Cleanse. Minimizing duplicate records, standardizing names, and validating details reduces errors during processing invoices. This step creates a stable foundation so automation delivers accurate and consistent results.
  • Integrate Vendor Data with BI Reporting. This gives finance teams real-time visibility into supplier relationships, discounts, and payment terms. With the right reporting tools, organizations can spot risks early and maximize cost savings across their vendor base.
  • Create Clear Governance Policies. Decide who will add, update, and maintain the vendor master file, and set basic approval rules for any changes. Clear guidelines keep vendor data consistent across the AP department and reduce the chance of errors slipping back in.

AP Automation Challenge 3: Inflexibility in Exception Handling

Most AP automation tools are built to process routine transactions quickly and consistently. But when something falls outside the expected pattern, many systems don’t know what to do next. This could include things like a missing PO, an invoice with mismatched amounts, or a supplier billing in a new currency. These exceptions often get flagged, but not resolved.

 

Without the right logic and escalation paths, exception queues become digital purgatory. Invoices stall. Teams spend hours chasing down approvals or clarifying mismatches. And because exceptions require manual review, they tend to pile up, undermining the very efficiency automation promised in the first place.

How Inflexible Exception Handling in AP Automation Can Impact Your Accounts Payable Operations

  • Supplier Strain: Delays in resolving exceptions can frustrate vendors, leading to late payments, increased inquiries, and damaged relationships—especially for key suppliers who expect reliable processing.
  • AP Department Overload: Instead of reducing workload, exception handling often becomes a bottleneck. AP teams spend more time manually resolving outliers than optimizing the process as a whole.
  • Missed Discounts and Cash Flow Disruptions: Exceptions interrupt payment timelines, which can lead to missed early payment discounts or late fees—both of which chip away at profit margins and disrupt forecasting.
  • Compliance Risks: When exception resolution isn’t governed by clear protocols, teams may override automated controls just to get invoices paid. This opens the door to noncompliance and audit exposure.

Accounts Payable Automation Solutions for Smarter Exception Handling

  • Use BI Tools to Flag Trends in Exceptions. Repeated exceptions often signal a deeper process or vendor issue. With the right business intelligence tools, teams can track exception frequency, identify root causes, and prioritize fixes.
  • Define Clear Exception Routing Rules. Build workflows that automatically escalate exceptions based on invoice type, value, or risk level. That way, high-priority issues are surfaced quickly without relying on manual triage.
  • Establish Standardized Resolution Protocols. Equip AP teams with a consistent process for managing exceptions—who to contact, what documentation is needed, and when to escalate. This keeps invoice processing moving, even when issues arise.
  • Create a Feedback Loop Between AP and Procurement. Many exceptions start with errors in purchase orders or contracts. Build regular reviews between AP and procurement teams to correct discrepancies at the source and reduce recurring issues.

Overcoming AP Automation Challenges with the Right Partner

At Illumis Global, we’ve spent nearly three decades helping premier global organizations overcome these exact AP automation challenges. Our experience with AP recovery audits, business intelligence tools, and supply chain consulting gives us a front-row seat to how companies stumble; and more importantly, how they thrive when AP automation is done right.

 

AP teams count on us because we count on people. Our team understands supplier behavior and can solve problems that software alone cannot. Combined with IQ technology and global reach across 175+ countries, we deliver clarity, control, and confidence.

 

Ready to start turning technology into a true driver of profit recovery and growth? Contact Illumis Global today.

Mary Olofsson, Audit Quality Manager, at Illumis Global Accounts Payable Recovery Audit firm

Mary Olofsson

Audit Quality Manager

Mary joined Illumis in 2013 as an analyst with a keen eye for identifying discrepancies, turning them into recoveries for our clients. During her tenure she developed into a Lead Analyst where she has been instrumental as an advisor not only to the audit teams, but also our client contacts to ensure an effective and productive experience. Mary has much experience in several of the largest ERP systems our clients use, allowing her to effectively work hand in hand with clients to resolve issues as they arise. This longstanding experience, aids in her ability with the analysts on individual skill building and knowledge sharing, as well as providing attentive detail to clients and suppliers.

Tony Brush

President / CEO

Working for Illumis for 21 years, Brush has been instrumental in the growth of the company. Brush served as Vice President at Illumis before stepping into the role of President / CEO and has been involved in all aspects of the company’s business throughout his career.

 

Brush’s approach to his role centers on the motto of Illumis, Bright Ideas for Better Profits. Known for his loyalty, team building, and tough but fair expectations, he empowers employees to deliver, therefore fostering a company culture that ensures customers can count on people.