Tips for Picking the Best Accounts Payable Automation Software

As technologies like machine learning (ML) continue to drive business growth, manual accounts payable (AP) workflows are becoming more costly and inefficient by the day. An AP automation software solution is now essential for staying competitive, yet many organizations still struggle to streamline their entire process.

Case in point: according to research by the Institute of Financial Operations and Leadership (sponsored by SAP), 74% of teams reported being only partially automated in 2024. For many of those who have yet to integrate fully, the main obstacle is finding the best solution to help them manage their workflows. 

This guide will give you tips for picking the best accounts payable automation software, exploring how these tools work, why they matter, and best practices for implementing them into your workflows.

Key highlights:

• Accounts payable (AP) automation software digitizes invoice capture, approvals, and payments to streamline the entire accounts payable workflow.
• Integration with your ERP, real-time visibility, and customizable workflows are critical for long-term success.
• The right tool reduces fraud risk, improves audit readiness, and scales alongside your business.
• ExFlow AP offers a native Dynamics 365 experience with AI-driven compliance, real-time insights, and flexible pricing built for enterprise teams.

What Is AP Automation Software?

Automated AP software digitizes invoice processing instead of the manual methods most companies still rely on. Rather than juggling spreadsheets, email approvals, and paper trails, everything happens in one system that handles invoices from start to finish.

The software reads invoice data from PDFs, scanned documents, and digital files that are received via email or upload portals. It compares this data against existing purchase orders or contracts to catch discrepancies early. It then gets routed for approval and payment or flagged for investigation when the numbers don’t add up. 

This approach replaces the old method of tracking invoices through spreadsheets, email threads, and filing cabinets. Automation helps teams:

• See exactly where each invoice sits in the approval workflow
• Streamline reports on spending patterns and vendor performance
• Create a comprehensive audit trail that improves compliance

Why Is Automated AP Software Critical for Teams in 2025?

For most finance teams, AP is still one of the most manual workflows. However, the right software doesn’t just speed things up; it transforms how departments operate, freeing up time, reducing errors, and giving leaders better control over spend.

The impact isn’t hypothetical, either. According to Ardent Partners’ 2025 AP trends report, enterprises using automation software report:

• Touchless invoice processing rates of 49.2%, more than twice the rate of their peers
• A 50% reduction in time spent answering supplier inquiries
• 59% fewer invoice exceptions compared to competitors

Together, these improvements show what’s possible when teams have the best AP automation solutions in place. It’s not just about doing more in less time; it’s also about building a finance function that’s smarter, more responsive, and ready to scale.

Why Choosing the Right AP Automation Software Is so Difficult 

Choosing the right software to handle enterprise AP automation isn’t as black and white as it seems, especially with so many solutions available on the market. The choice isn’t liable to get any easier in the foreseeable future, as research by IndustryARC estimates the market size to reach $17.4 billion by 2031, growing at a CAGR of 14.0% from 2025 to 2031. 

The biggest challenges, however, can come from within your organization. These issues include:

Lack of Well-Documented Policies

Automation can improve how your department works, but it won’t fix bad accounts payable processes. If your current policies have problems, automation just makes those problems happen faster and more consistently.

You might run into issues like invoices getting sent to the wrong people or getting stuck waiting for approval. Your payment processing rules might contradict each other, or you might have so many exceptions that people still need to handle things manually. Different teams or offices might process invoices in entirely different ways.

An end-to-end AP automation solution and payment optimization strategy work best when you already have transparent, working processes. Otherwise, you’re just automating chaos.

Poor Visibility into Current Spending

An automated AP solution only works if you know what’s going on with your spending right now. Most teams don’t have real-time visibility into their data because they’re using different systems that don’t talk to each other, categorize things differently, or make mistakes entering information.

These discrepancies show up in different ways. For example, you might have invoices coming through several systems without a single view. People might name vendors or code expenses differently, which throws off your spending reports. Worse still, data could get entered late, ensuring that your financial picture is always behind. 

Without clean, current data, you won’t know if automation is actually helping or just moving the problems around faster.

Implementation Errors

Getting AP automation up and running isn’t necessarily straightforward. Your existing data might be messy or stored in formats that are difficult to transfer. Also, legacy systems often don’t integrate well with new software, so you end up building custom connections or moving information between platforms.

Not to mention, training usually becomes a bigger project than most companies expect. People need time to adjust how they work, but the real challenge is discovering that your “standardized” processes aren’t standard at all. Different departments have developed their workarounds and exceptions over the years, even though everyone thought they were following the same procedures. 

Internal and External Resistance 

Not all implementation challenges are technical. Your team might resist new software because they’re used to doing things a certain way, even when it takes longer or causes problems. This attitude is fair if you consider that people get nervous about learning new systems, and some worry that automation means their job is at risk.

Vendors can be reluctant to change, too. Some like the current setup because it benefits them. They might get paid faster because they have good relationships with your AP staff, or they’ve set up their billing processes to work with your manual system. As a result, they might be slow to adapt their invoicing practices or reluctant to follow new submission requirements.

How to Choose AP Automation Software: Key Features to Consider 

When selecting the top AP automation solutions, there’s much to consider beyond the initial cost. From ease of use to seamless integration within your existing systems, choosing the wrong solution wastes resources and erodes your budget.

So, what should you be looking for? Here are the six top tips for picking the best accounts payable automation software for your enterprise:

1. Integration With Your ERP and Accounting Systems

Here is the first question you should ask: Can the AP automation software integrate with existing ERP systems? Poor connectivity means your data gets stuck in separate tools, and people end up doing manual work to move information around. That defeats the whole point. Native solutions work better than custom setups that need to be reconfigured when you update either system.

Make sure your solution has:

• Direct data sync
• Automatic updates
• Compatibility with your ERP version and modules

2. OCR and Intelligent Data Capture

Most vendors show off their OCR technology using perfect documents, but that’s not reality. The software should be able to read invoices correctly, even when they’re bad scans, handwritten, or come in weird formats.

Test invoice data capture with actual documents from your vendors before making a purchase, as you want software that can:

• Handle different file types and poor scan quality
• Get better at reading invoices when you correct their mistakes
• Pull out vendor names, amounts, dates, and line items consistently

3. Customizable Approval Workflows

Your company’s approval process won’t match whatever the software came set up with out of the box. Rigid systems force you to change how your business works instead of the other way around. You need to be able to set up rules that match your actual approval chain and spending policies.

Look for streamlined AP systems that let you:

• Route your invoices based on dollar amounts, departments, or vendors
• Set a backup approval process when someone is on vacation or sick
• Change the approval web yourself without calling IT every time

4. Security and Compliance

You’re dealing with financial data and vendor payment information that requires security. Beyond simply protecting your system from possible breaches, auditors and regulators will want to see who accessed what and when. Different employees should only see the data they need for their jobs.

Ensure your automated AP software enables:

• User permissions that limit access based on roles
• Data encryption for storage and transmission
• Complete logs and audit trails of your entire system

Automated systems also work to detect and prevent fraud actively. Research from PYMNTS found that enterprises with automated systems in place lost 2% of their annual revenue to fraud, while competitors lost 4.5%.

5. User Experience and Support

Is the AP Automation software easy to use? This should be the first question you ask yourself. If the software is confusing or breaks frequently, people will find ways around it or just go back to their old methods. You need something that works when your team uses it every day. Test it with the people who will be clicking through it, not just the IT department.

You want an AP automation tool that has:

• A simple interface that doesn’t require weeks of training
• Available support teams that know AP workflow processes, not just technical troubleshooting
• Regular updates and maintenance that happen without disrupting your work

6. Scalability and Analytics

Your invoice volume will probably grow over time, and you’ll want more than just basic transaction processing. The AI-powered AP automation software you choose should handle more invoices without slowing down, and provide valuable insights about your spending patterns and vendor relationships.

Your AP software should offer:

• Performance that holds up when invoice volume increases
• Reporting tools that show spending trends and vendor performance
• Continuously updated integration with other business systems as your needs (and the market) change

Implementing the Best AP Automation Systems for Enterprise Companies: Best Practices

Choosing the best AP automation software is half the battle. Implementation is just as critical to ensure the success of your solution. Keep the best practices below in mind as you begin to streamline your processes.

Clean Up Your AP Workflow First

Before anything goes live, ensure you tighten up your workflow, aligning naming conventions, approval limits, and how exceptions get handled. If the process is inconsistent or full of hacks, the system won’t know what to automate. Remember, clean inputs ensure clean outputs.

Start with One Specific Invoice Use Case

Pick a single department or invoice type and get that working first. Start small so you can fix problems without affecting your entire AP process. Once the system is running smoothly for a few months and people are comfortable with it, you can expand to other departments or add more invoice types.

Prepare Vendors for the Changes to Your AP Process

If vendors don’t know what’s changing, they’ll keep sending invoices as they have in the past. That’s how exceptions pile up. Send a quick breakdown of what’s different, what you need from them, and when it kicks in. Make it easy, and give them a contact for questions.

Train Your Staff with Real Invoice Examples

Train people with actual invoices they’ll see, not demo samples. Walk them through what changes in their work and let them ask questions. Be available after you launch the system because people will have more questions once they start using it daily. New employees might need extra training sessions.

Set Access and Permissions for Your AP Automation Solution

Assign user roles before anyone logs in. Give people access to what they need and nothing more. Use role-based permissions, enable two-factor authentication, and turn on activity logging, as these controls help protect financial data and create a clear audit trail for internal reviews.

Monitor Early Automation Metrics Closely

Track invoice volume, approval times, and error rates as you go. When something looks wrong, figure out what’s causing it and fix it right away. You might need to change some approval rules, provide additional training, or adjust how certain types of invoices get processed. The system will need tweaking as your business changes and grows.

Keep Optimizing Your Automation After Launch

The rollout isn’t done when the system goes live. It’s just getting started. Keep a pulse on what’s working — and what’s not — by tracking real transactions. If approvals stall or AP teams start skipping steps, you’ll catch it early and can course correct before bad habits lock in.

ExFlow Is the Best AP Automation Software for Enterprises

ExFlow AP runs natively in Dynamics 365 Finance & Operations and Business Central, so you can streamline processes without third-party tools and manage everything where your accounting data already lives.

Our comprehensive automation solution offers:

• Streamlined invoice capture, approvals, and line-level matching to reduce errors
• AI to detect potential fraud and enforce regulatory compliance across workflows
• Minimized supplier inquiry times with fast status updates and self-service access
• Complete visibility from invoice receipt to payment in one centralized view
• Flexible pricing that scales with your organization

Book a demo and see how ExFlow’s AP automation software solution can help your enterprise save both time and money.