AthenaHealth RCM Optimization: How to Maximize Revenue on the Athena Platform

By Medtransic | February 16, 2026 | 12 min read

Quick Summary: Using AthenaHealth but still seeing high denial rates? Learn how to optimize your Athena workflows, clean up your hold buckets, and leverage AthenaCollector for maximum revenue.

AthenaHealth is one of the most widely adopted EHR and practice management platforms in healthcare, serving over 160,000 providers across the country. The platform offers a powerful combination of clinical documentation, medical billing, and revenue cycle management tools that promise to streamline operations and improve financial performance. But there is a significant difference between having AthenaHealth and actually using it well.

The reality is that most practices running on Athena are leaving substantial revenue on the table — not because the platform lacks capability, but because their workflows, rules, and configurations were never optimized after initial implementation. Hold buckets fill up with claims that no one works. The rules engine runs on default settings that catch obvious errors but miss specialty-specific coding patterns. Charge capture workflows have gaps that let billable services slip through undocumented. And the powerful reporting tools sit untouched while revenue problems compound month after month.

At Medtransic, we work with practices on the AthenaHealth platform every day. We have seen what separates high-performing Athena practices from those struggling with denials and slow collections. This guide walks through the specific areas where Athena optimization delivers the biggest revenue impact — and the configuration mistakes that cost practices tens of thousands of dollars annually.

The Revenue Gap on the Athena Platform

AthenaHealth markets its platform as a revenue cycle management solution, and the built-in AthenaCollector module does provide end-to-end billing functionality. But the platform is a tool, not a strategy. The difference between a practice collecting 92 percent of expected revenue and one collecting 97 percent comes down to how Athena is configured, monitored, and managed on a daily basis.

The most common revenue gaps we find in Athena practices fall into five categories:

• Claims sitting in hold buckets for days or weeks without being worked, missing timely filing deadlines
• Default rules engine settings that are too generic for the practice's specialty mix, allowing preventable denials to pass through
• Charge capture workflows that do not prompt providers for billable services performed but not documented, such as chronic care management or transitional care
• Denial workqueues that grow faster than staff can clear them, creating a backlog of recoverable revenue that ages past appeal deadlines
• Underutilized reporting dashboards that could identify systemic issues but are never reviewed

Each of these gaps is fixable. None of them require switching platforms. They require someone who understands both the clinical billing requirements of your specialty and the technical configuration of the Athena platform — and that combination of expertise is rare in general billing operations.

Hold Bucket Management: Where Claims Go to Die

The hold bucket system in AthenaHealth is designed to catch claims that need attention before submission — missing information, coding conflicts, eligibility issues, or authorization requirements. In theory, this prevents dirty claims from going out. In practice, hold buckets become the single largest source of revenue delay and loss for most Athena practices.

The problem is not that claims land in hold buckets. The problem is what happens next. In a well-optimized practice, hold bucket claims are reviewed and resolved within 24 to 48 hours. In the average Athena practice, claims sit in hold buckets for 5 to 14 days — and some never get worked at all. Every day a claim sits in a hold bucket is a day your practice is not getting paid.

Effective hold bucket management requires three things:

• Daily review protocols with assigned ownership for each hold reason category
• Threshold alerts that escalate when hold bucket volume exceeds normal levels, indicating a systemic issue rather than individual claim problems
• Root cause analysis of the most common hold reasons to eliminate recurring issues at the source rather than resolving them one claim at a time

For example, if 30 percent of your hold bucket claims are flagged for missing referring provider information, the fix is not to manually add the referring provider to each claim. The fix is to update your scheduling and intake workflows to capture that information before the encounter. This is the kind of upstream problem-solving that turns hold bucket management from a daily firefight into a declining workload.

Rules Engine Optimization: Stop Preventable Denials Before Submission

AthenaHealth's rules engine is one of the platform's strongest features — when configured correctly. It evaluates every claim against a set of coding, billing, and payer-specific rules before submission, flagging issues that would result in denials. But out of the box, the rules engine runs on Athena's default rule set, which covers broad coding guidelines and common payer requirements.

For general primary care billing, the default rules may catch 70 to 80 percent of preventable denials. For specialty practices — cardiology, orthopedics, gastroenterology, dermatology — the default rules miss a significant portion of specialty-specific coding errors because they are not programmed to evaluate the nuances of those code families.

Custom rules engine configuration means adding rules that catch specialty-specific issues:

• Modifier validation rules that flag missing TC/26 modifiers on diagnostic imaging studies
• Bundling edit rules that check for common CCI edit pairs specific to your specialty's procedure mix
• Authorization requirement rules based on your actual payer contracts, not generic Athena defaults
• Frequency limitation rules that prevent submission of services that exceed payer-specific visit or procedure limits
• Place of service validation rules that ensure facility vs. non-facility rates are billed correctly

Building a specialty-tuned rules engine takes expertise in both the clinical coding requirements and the Athena platform's rule configuration interface. It is not a one-time setup — rules need to be updated as payer policies change, new CPT codes are released, and your practice's service mix evolves. This ongoing maintenance is where most practices fall behind because they lack the dedicated resources to monitor and update their rules engine regularly.

Charge Capture Workflows: Closing the Documentation Gap

Charge capture is the process of translating clinical services into billable claims. In AthenaHealth, charge capture happens when providers close their encounters and billing staff review and finalize the charges. The gap between what was clinically performed and what ends up on the claim is one of the most costly — and most invisible — revenue leaks in any practice.

Common charge capture failures on the Athena platform include:

• Providers selecting E/M codes below the documented level of complexity, resulting in systematic undercoding across hundreds of visits
• Billable ancillary services performed during the visit but not added to the encounter charge list — injections, wound care, diagnostic tests
• Time-based services like prolonged care codes that require explicit time documentation which providers forget to enter
• Separately billable components of complex procedures that providers assume are included in the primary procedure code
• Missed opportunities for add-on codes and separately reportable services that could increase per-visit revenue by $50 to $200

Optimizing charge capture on Athena involves configuring encounter templates with specialty-specific charge prompts, building smart lists that suggest commonly paired codes based on the primary procedure, and implementing regular coding audits that compare clinical documentation against submitted charges to identify patterns of undercoding. When Medtransic onboards an Athena practice, charge capture gap analysis is one of the first areas we evaluate because the revenue impact is immediate and measurable.

Denial Workqueue Strategy: How to Actually Clear Your Denied Claims

AthenaHealth organizes denied claims into workqueues — categorized lists of claims that need action based on denial reason, payer, age, and dollar value. The workqueue system is well-designed for organizing denial management work, but most practices use it reactively rather than strategically.

The reactive approach is to work the denial workqueue from top to bottom, resolving whatever claim appears next. This feels productive but is inefficient because it treats a $15 denial the same as a $1,500 denial, and it fails to identify patterns that could prevent future denials of the same type.

A strategic denial workqueue approach prioritizes by:

The single most impactful change most Athena practices can make to their denial management is shifting from reactive claim-by-claim resolution to pattern-based root cause elimination. When you fix the upstream issue causing 50 denials per month, you save exponentially more time and money than resolving those 50 denials individually after they occur. This approach requires someone who understands both revenue cycle management strategy and the Athena platform's denial analytics tools.

AthenaHealth Reporting: Using Data to Drive Revenue Decisions

AthenaHealth provides a robust reporting and analytics suite that most practices barely scratch the surface of. The standard reports — daily charges, monthly collections, AR aging — provide a basic financial picture. But the real power of Athena's reporting lies in the operational and clinical metrics that identify revenue optimization opportunities before they become visible in the financial statements.

Key reports that every Athena practice should be monitoring weekly include:

• Denial rate by payer and denial reason code — to identify which payers are denying most frequently and why
• Days in AR by payer — to spot payers whose payment velocity is slowing, indicating potential credentialing or contract issues
• Clean claim rate — the percentage of claims that pass through the rules engine without holds, which directly correlates with revenue cycle speed
• Charge lag report — the time between date of service and charge entry, which reveals delays in provider documentation or charge capture workflows
• Collection rate by provider — to identify providers whose coding patterns may be contributing to underpayment or higher denial rates

These reports are available within the Athena platform, but interpreting them and translating findings into operational changes requires billing and RCM expertise. A declining clean claim rate, for example, could indicate a rules engine configuration issue, a new payer policy change that has not been accounted for, a staffing problem in your front office, or a documentation issue with a specific provider. Knowing which signal to investigate first — and what action to take — is where end-to-end RCM expertise becomes essential.

Real-Time Eligibility Verification: Preventing Front-End Denials

AthenaHealth includes real-time eligibility verification that can check patient insurance coverage before or at the time of the appointment. This is one of the most underutilized features on the platform, despite the fact that eligibility-related denials account for 20 to 30 percent of all claim denials across the industry.

The most common eligibility-related issues that lead to denials include:

• Patient insurance coverage that lapsed or changed employers between scheduling and the appointment date
• Incorrect subscriber ID or group number entered during registration
• Coordination of benefits errors where the primary and secondary payer order is incorrect
• Out-of-network services rendered without proper patient notification or authorization
• Retroactive Medicaid eligibility that requires re-billing after coverage is confirmed

Configuring Athena to run automated eligibility checks 48 hours before each scheduled appointment — and flagging patients whose coverage cannot be verified — gives your front office time to contact the patient, update insurance information, and obtain any necessary authorizations before the visit. This single workflow change typically reduces eligibility-related denials by 40 to 60 percent and eliminates the most frustrating type of claim rejection: the one that could have been prevented with a two-minute phone call before the patient walked in the door.

5 Common AthenaHealth Configuration Mistakes That Cost You Money

After working with dozens of practices on the Athena platform, Medtransic has identified five configuration mistakes that appear in the majority of underperforming Athena implementations:

None of these mistakes are unique to any single practice size or specialty. We see them in solo practices and multi-provider groups alike. The difference is that larger practices lose proportionally more money because each mistake compounds across higher claim volumes.

How Medtransic Optimizes Athena for Maximum Revenue

Medtransic provides dedicated AthenaHealth RCM optimization as part of our medical billing services. Our approach is built on the understanding that AthenaHealth is a powerful platform that delivers strong results when properly configured and actively managed — but it requires ongoing attention from people who understand both the platform and the clinical billing requirements of your specialty.

Our Athena optimization process includes:

• Comprehensive configuration audit of your current Athena setup — rules engine, hold bucket structure, charge capture workflows, reporting dashboards, and eligibility verification settings
• Specialty-specific rules engine customization based on your practice's top denial reasons and the coding patterns unique to your specialty
• Hold bucket management protocols with daily monitoring, assigned ownership, and root cause analysis to reduce hold volume over time
• Charge capture gap analysis comparing clinical documentation against submitted charges to identify systematic undercoding or missed services
• Denial workqueue strategy with prioritization by dollar value, appeal deadline, and pattern identification
• Monthly reporting reviews with actionable recommendations based on Athena analytics data
• Ongoing rules engine updates as payer policies change, new CPT codes are released, and your practice's service mix evolves

The result is a practice that collects more of what it earns, submits cleaner claims, resolves denials faster, and uses data to continuously improve its revenue cycle performance — all within the AthenaHealth platform your team already knows. If your practice is on Athena and you suspect you are leaving money on the table, contact Medtransic for a no-obligation review of your current Athena configuration and revenue cycle metrics.