Why Bill.com problems keep growing for modern AP teams

If you are feeling daily friction with Bill.com, you are not imagining it. Many finance leaders start with Bill.com, then hit a wall as volume, complexity, and stakeholder expectations grow. What starts as a convenient bill pay tool turns into a source of bill.com problems, approval bottlenecks, and constant AP software frustrations.

Modern AP teams want more than faster data entry. You need control, visibility, and clean data that you can trust. When those are missing, the result is late nights, messy reconciliations, and tense conversations about “where the cash actually went.”

This guide breaks down why Bill.com is not working for many modern AP teams anymore, the common bill.com issues you may recognize, and how a purpose-built AP platform like MakersHub can help you scale with confidence instead of duct tape.

The real cost of Bill.com problems for finance teams

On paper, Bill.com solves a clear problem: digitize vendor bills, speed up payments, and reduce paper checks. For simple AP environments, it can work well.

But as teams grow and operations get more complex, several hidden costs start to show up.

• You still do manual cleanup because header-only data capture does not give you real job, class, or project detail.
• You maintain “side systems” in spreadsheets, shared drives, and email to track what Bill.com cannot.
• You spend time chasing approvals and re-keying information instead of reviewing results and advising the business.
• You are never fully sure whether the accounting system reflects what actually happened in AP this week.

The biggest problem is not that Bill.com is “bad.” It is that it was never designed to be the system of record for complex AP workflows. It is a bill payment tool. Modern AP teams need an automation and control layer that reaches across the full lifecycle, from intake and coding to multi-step approvals and payment authorization.

Common Bill.com issues that show you have outgrown it

If any of these feel familiar, you are living with Bill.com issues that will only get louder as you grow.

1. Limited data extraction means you are still in spreadsheets

For many teams, Bill.com captures header data only. You get vendor, invoice number, date, and total. The rest of the work is still on you.

That creates several downstream AP software frustrations:

• You cannot reliably map line items to jobs, customers, or classes.
• Materials, labor, and freight get lumped together at the expense level.
• You add manual notes, export to spreadsheets, and run side-car reports for project managers or leadership.

When you are managing construction projects, multi-location operations, or detailed grant programs, totals are not enough. You need quantity, SKU, unit price, and line-level coding to understand true cost drivers.

How MakersHub handles it

MakersHub ingests every bill or receipt and extracts full line-item detail using purpose-built AI. Quantities, SKUs, item descriptions, GL codes, jobs, classes, and customers can be auto-detected or auto-mapped. That data syncs cleanly into your accounting system so you see real costs, not just totals, without manual entry.

2. Rigid approvals that ignore real-world context

Bill.com approvals often center on simple dollar thresholds and basic routing. For a small team, that can be fine. For complex operations, it falls short.

Real-world approvals are more nuanced:

• Some vendors require specific reviewers, regardless of invoice amount.
• Certain GL codes or locations need department head sign off.
• Projects or customers require project manager approval even on smaller bills.
• Sensitive spend should go through multiple approvers before payment is authorized.
  

When your tool cannot support that context, teams patch together “approvals” in email and Slack, then try to mirror them inside Bill.com later. The result is extra work and a weaker audit trail.

How MakersHub handles it

MakersHub supports contextual, multi-step approvals that can route based on:

• Vendor
• Amount thresholds
• GL code, class, or location
• Customer or project
• Purchase order and receipt status

You can separate bill validation from payment authorization, enforce true segregation of duties, and still keep workflows fast and lightweight for approvers.

3. Bundled approvals and payments that hide errors

Another source of bill.com problems is the way approval and payment are often bundled together in practice. It becomes one motion: “approve to pay.”

That sounds efficient, but it blurs two different questions:

• Is this bill valid, coded correctly, and ready to post.
• Should we pay this bill now, in full, from this account.

When those decisions happen in a single click, errors slide through:

• Overpayments when quantities or pricing do not match the PO.
• Duplicate invoices that look slightly different.
• Bills that should be held due to project disputes or cash constraints.

By the time anyone notices, the money is gone and you are backtracking.

How MakersHub handles it

MakersHub separates bill approval from payment authorization by design. Finance teams can:

• Validate and approve bills for posting.
• Decide later what to pay, when, and from which bank account.
• Use three way matching and automated checks to validate pricing, quantities, and terms.

You gain more control without slowing down the process.

4. AP software frustrations with vendor experience

Vendors are a critical part of your AP workflow. When their experience is clunky, you pay the price in follow-up emails, phone calls, and strained relationships.

Common complaints finance teams hear:

• Vendors must create an account or log in to track payments.
• Remittance is unclear or missing.
• It is hard for them to match payments to specific invoices.

When support tickets from vendors pile up, your team becomes the help desk for a tool you do not control.

How MakersHub handles it

MakersHub focuses on vendor clarity without forcing new logins:

• Vendors receive clear remittance emails showing exactly what was paid and what remains open.
• Payments are trackable, from initiation through deposit.
• There is a direct link back to underlying bills so your team can answer questions quickly.

You get fewer “where is my payment” calls and better vendor loyalty.

5. Integration friction and reconciliation headaches

Many teams adopt Bill.com expecting smooth integration with their accounting system. In practice, they end up wrestling with:

• Confusing one way vs two way sync settings.
• Data that flows in one direction, forcing manual updates in the other.
• Duplicate or missing records that show up during month end close.

You may find yourself double checking every sync, manually matching payments, and reconciling out-of-sync vendor balances.

How MakersHub handles it

MakersHub is built around deep, two way sync with QuickBooks Online and QuickBooks Desktop. As well as Sage Intacct. Bill data, approvals, and payments flow cleanly in and out:

• Bills created or updated in MakersHub sync into your accounting software with line-item detail and coding.
• Payments recorded in MakersHub create or update payment records in your accounting software.
• Vendor, item, and account changes stay aligned between systems.
  

You get a single source of truth instead of two systems that constantly drift apart.

6. Pricing that punishes growth

A common source of bill.com issues is pricing complexity. Per user fees, per payment fees, and add ons for features you thought were standard can make costs unpredictable.

For growing teams, this can lead to tough tradeoffs:

• Limiting user seats to save money, which slows approvals.
• Avoiding extra features, even when they would improve control.
• Surprise invoices when volume spikes in busy months.

The tool that was supposed to make AP scalable starts to feel like a tax on growth.

How MakersHub handles it

MakersHub pricing is built for teams that expect volume to increase:

• Clear plans that scale with bill volume, not every click or user.
• Payment automation included without surprise fees for basic rails.
• A Business Master plan for high volume, multi-entity teams that need unlimited users and advanced workflows.

You can confidently add approvers, bring more vendors into the system, and expand services without worrying about a new invoice for every seat.

What modern AP teams actually need instead of more bill.com workarounds

If you are feeling these AP software frustrations, the answer is not “more training” or “another round of process docs.” You likely need a different category of tool.

Modern AP teams need:

• Clean, structured data at the line-item level that can feed into job costing, forecasting, and analytics.
• Contextual approvals that reflect how your business actually operates, not just invoice totals.
• Separation of duties between bill validation and payment authorization.
• Reliable integrations that treat your accounting platform as the source of truth.
• Transparent vendor communications that do not require new portals.
• Predictable pricing that respects the fact that you are scaling, not staying small.
  

This is exactly the gap MakersHub was built to fill.

MakersHub: turning AP into a strategic advantage instead of a daily grind

MakersHub automates and simplifies accounts payable for businesses with complex operations and high payment volumes. Instead of just moving bills into a digital queue, it solves the clean data problem first.

At the core is WiseVision, a purpose-built AI stack that:

• Extracts dramatically more information from bills than legacy OCR.
• Structures and indexes that data so it is usable across workflows.
• Learns vendor formats, line-item patterns, and coding rules over time.

From there, MakersHub delivers:

• Automated bill capture from any format, including PDFs, images, scans, and multi-page documents.
• Line-item level coding to GL accounts, jobs, customers, classes, and locations.
• Configurable approval workflows that fit each client, entity, or department.
• Separate bill approval and payment authorization for stronger control.
• Two way sync with QuickBooks Online, QuickBooks Desktop, and Sage Intacct.
• Payment automation across ACH and checks, with full traceability and vendor friendly remittance.

You get an AP system that is built for the way modern teams actually operate, not for the simplest possible use case.

Case study: how Outsourced FinOps scaled past Bill.com with MakersHub

If you are wondering what this looks like in the real world, Outsourced FinOps is a strong example.

About Outsourced FinOps

Outsourced FinOps is a full stack finance partner to architecture, engineering, and construction firms. They handle managed accounting, payroll operations, project reporting, and more, with a focus on complex, project-based businesses.

As the client roster grew, so did AP complexity:

• Hundreds of bills and thousands of line items per client.
• Multi layer approvals across owners, project managers, and finance.
• Tight visibility requirements on project and job level costs.

They started with BILL, but it quickly showed its limits.

“BILL is fine if you just need a simple bill pay tool. But when you have high volume and complex needs, it starts to break down. We needed better controls for approvals and payment authorization, and more visibility into all that data.”
– Michael Newberger, Founder and CFO, Outsourced FinOps

Why they chose MakersHub

After evaluating alternatives, Outsourced FinOps chose MakersHub for three reasons:

• AI powered line-item extraction that eliminated manual data entry.
• Configurable approvals and payment controls that matched how clients really worked.
• Predictable pricing that did not explode as they added more complex clients and approvers.

Onboarding was smooth across their client portfolio, regardless of volume or complexity.

The results

With MakersHub, Outsourced FinOps achieved:

• A 10x reduction in the time spent processing bills.
• Zero manual data entry thanks to accurate line-item extraction.
• Full audit trails for every approval, payment, and transaction.
• Real-time visibility into when money leaves, when it reaches the vendor, and when it is deposited.

“The work of processing bills has decreased by 10x. That faster speed directly impacts our bottom line because we do not have to bake in the cost of manual data entry anymore. I also know exactly when money leaves, when it is sent to the vendor, and when it is deposited. Every step is tracked, which is critical for the clients we serve.”
– Michael Newberger, Founder and CFO, Outsourced FinOps

If you want the full story, you can read the Outsourced FinOps customer case study.

How to tell if you are ready to move beyond Bill.com

You do not need to dislike Bill.com to outgrow it. Many teams simply reach a point where a bill pay tool is not enough.

You are likely ready for a different AP platform if:

• You export data into spreadsheets every week to get the level of detail you need.
• Approvals still happen in email chains, Slack messages, and side conversations.
• You cannot easily separate who approves bills from who authorizes payments.
• Project managers or leaders complain that they cannot see real-time costs.
• Vendors keep asking for payment status and better remittance details.
• Your Bill.com invoice gives you anxiety because you are not sure why it is so high.

If three or more of these feel true, it is time to explore alternatives that treat AP as a strategic system, not just a bill pay utility.

How modern teams replace Bill.com with MakersHub without disruption

Switching AP tools can feel risky. The good news is that the right platform should make migration straightforward and low stress.

A typical MakersHub migration from Bill.com looks like:

1. Discovery and design
   
   • Map your current AP workflows, approval paths, and accounting setup.
   • Identify what Bill.com is doing well and where the gaps are.
   • Design contextual approval flows and payment controls in MakersHub that mirror how your team actually works.
     
     
2. Configuration and integration
   
   • Connect MakersHub to your accounting system.
   • Turn on AI powered data extraction and auto-mapping.
   • Configure approval groups, thresholds, and routing rules.
     
     
3. Pilot and scale
   
   • Start with one entity or client to validate the workflow.
   • Train approvers on simple, email-based or in app approvals.
   • Roll out to additional entities or clients once the pattern is proven.

Because MakersHub is designed for complex AP, teams typically see value in the first month: faster bill processing, cleaner data in the ledger, and clearer visibility into cash. Book your live demo now. 

FAQ: Bill.com problems and moving to a modern AP platform

What are the most common Bill.com problems for modern AP teams?

The most common issues are limited line-item data capture, rigid approval workflows based mainly on invoice totals, clunky integration behavior with accounting systems, vendor frustration with portals and logins, and pricing that becomes unpredictable as volume grows. These problems tend to intensify as your operations expand.

Do I have to replace Bill.com completely to use MakersHub?

Most teams that move to MakersHub use it as their primary AP automation and control layer, from bill intake through payment. If you have scenarios where Bill.com is still useful for simple workflows, you can keep it in a limited role, but the goal is usually to consolidate on one platform that can handle complex AP at scale.

How does MakersHub handle data migration from Bill.com?

MakersHub connects directly to your accounting system, which remains your system of record. You do not have to “move” historic transactions out of Bill.com. Instead, you begin routing new bills through MakersHub, which syncs cleanly into your ledger. Historic documents can stay where they are while you standardize everything going forward.

Will approvers and vendors need new logins with MakersHub?

Approvers can review and approve bills directly from email or in the MakersHub app, depending on your preferences. Vendors do not need to create logins. They receive clear remittance emails and can get payment details through your team without a separate portal experience.

Is MakersHub secure enough for high volume AP operations?

Yes. MakersHub is built for high volume, multi-entity AP with security controls that include role-based access, granular permissions, audit logs, and secure payment workflows. You can enforce separation of duties, restrict who can approve or release payments, and maintain an audit-ready trail of every action taken in the system. MakersHub is also SOC2 compliant. 

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