APM Performance Pathway (APP) Reporting: 4 Critical Lessons ACOs Must Learn Before It's Too Late

Welcome to the Reality of APP Reporting

The landscape of quality reporting for Accountable Care Organizations (ACOs) has undergone a seismic shift. As of 2025, the CMS Web Interface has been officially retired, and APM Performance Pathway (APP)reporting is now mandatory. This transition represents more than just a change in reporting mechanisms—it's a fundamental transformation in how ACOs must approach quality measurement and reporting. It’s also important to understand that CMS now requires ACOs to use a Qualified Registry vendor for quality reporting submissions, adding another critical layer of planning and partnership to the process.

Over the past year, ACOs have been weighing which reporting path best fits their needs: MIPS Clinical Quality Measures (CQM), Medicare CQM (MCQM), or eCQM reporting. MCQM offers a smaller required reporting population, while CQM and eCQM come with greater complexity and demand a more advanced infrastructure to support broader, all-patient reporting requirements.

Regardless of the option selected, many ACOs significantly underestimated the scope and complexity of APP reporting—an issue that became clear when CMS released its final 2024 Medicare CQM patient lists. According to Healthcare Financial Management Association, only 16% of eligible MSSP ACOs used eCQMs/CQMs in 2023, indicating that most organizations found the transition to APP a "significant" or "very significant" operational challenge.

This article draws from real-world experiences and data to help ACOs avoid critical pitfalls as they navigate APP reporting in 2025. The clock is ticking with the first quarterly files due out soon—the time to act is now.

Lesson #1: The Reporting Volume Can Double or Triple—Fast

Perhaps the most alarming discovery for many ACOs has been the sheer volume of patients requiring reporting under the new APP framework. The misconception that reporting would be limited to ACO attributed beneficiaries has led to significant operational strain.

The Volume Reality

Many ACOs transitioning to APP reporting have seen their quality reporting populations increase substantially compared to their attributed Medicare beneficiary populations. ACOs have faced reporting requirements for populations much larger than their attributed membership.

A real-world example comes from a mid-sized ACO with approximately 60,000 attributed members that ultimately had to report on more than 120,000 Medicare beneficiaries. This dramatic expansion created substantial workflow challenges, resource constraints, and operational stress that could have been mitigated with better advance planning.

The Quarterly Progression Trap

One particularly dangerous pattern we've observed is the false sense of security created by early quarterly files. Q1 patient lists often appear manageable, leading ACOs to delay comprehensive planning. However, as the year progresses, these lists commonly expand dramatically:

• Q1 typically represents only a fraction of what will ultimately become the final reporting population
• By Q3, most ACOs see a majority of their final reporting volume
• Q4 brings the remaining patients, often including the most complex cases with limited documentation

CMS data indicates that final MCQM patient lists often include significantly more patients than the initial Q1 lists. This growth trajectory means ACOs must plan capacity based on projected final volumes, not early-quarter estimates.

The implications of this volume surge go beyond simple logistics. Workforce strain, data collection bottlenecks, and coordination challenges can quickly compromise reporting quality and completeness if not anticipated.

Key Takeaway: Do not delay planning based on Q1 estimates. Instead, assume Q1 is just the beginning and prepare as if your final list will match or exceed last year's volume. The first quarterly file for 2025 is due out at the end of May—time to act decisively.

Lesson #2: Data Automation Is No Longer Optional

The scale of APP reporting has rendered manual approaches obsolete. With reporting populations frequently exceeding 100,000 patients across numerous care settings, manual chart abstraction is simply not viable. According to MDinteractive, automation through supplemental data feeds from Electronic Medical Records (EMRs), laboratories, and billing systems is now a necessity, especially for non-assigned patients.

The Automation Imperative

According to CMS, ACOs that implement automated data collection solutions for quality reporting achieve significant reductions in manual abstraction hours compared to those still relying primarily on manual processes. Moreover, automated approaches tend to result in improved measure performance rates, likely due to more comprehensive data capture.

Best practices now center on implementing supplemental data feeds from multiple sources:

• EMRs (both primary care and specialists)
• Laboratory systems
• Billing and claims systems
• Health information exchanges (HIEs)
• Patient registries

This multi-faceted approach is particularly critical for non-assigned patients, where claims data alone is insufficient for comprehensive measure reporting.

Integration Complexities

The implementation of automated data collection faces several significant hurdles:

• EMR Variation: EMRs differ significantly in capabilities and support for data sharing. While most ACOs use certified EHR technology, interoperability remains a major hurdle, with many reporting challenges integrating external data. ACOs must dedicate effort to validating their extracts—like QRDA-1 and other clinical data formats—accurately reflect required measures. Close collaboration with a registered quality reporting vendor is essential to ensure proper data feed implementation and compliance.
• Multi-System Requirements: The use of multiple EHR systems across ACOs presents significant challenges in aggregating and reporting quality measure data. According to AJMC, aggregating electronic clinical quality measure (eCQM) data from these disparate systems requires substantial effort, including manual processes and coordination with various EHR vendors.
• Provider Buy-In: Data sharing across organizational boundaries requires provider engagement. Many physicians cite concerns about additional administrative burdens as a barrier to sharing patient data for quality reporting purposes.

Some ACOs submitted partial or incomplete data in 2024 as a test approach. While this revealed valuable insights, it also resulted insignificant quality score penalties that could have been avoided with more comprehensive preparation.

Key Takeaway: Begin implementing automated data collection immediately. Prioritize EMR integrations first, followed by lab and billing system connections. Manual processes should be reserved only for exception handling, not primary data collection.

Lesson #3: EMR Coordination is a Full-Time Job

Even with a commitment to automation, the coordination of EMR data feeds has proven to be far more complex than most ACOs anticipated. Data feeds must be mapped, validated, and continually quality assured—it's far from a simple plug-and-play solution.

Critical Friction Points

The most common challenges in EMR coordination include:

• Incorrect Data Outputs: Many EMRs are not properly configured to generate the specific data elements required for current Clinical Quality Measure (CQM) specifications. Research consistently shows that custom configuration is often necessary to ensure accurate quality reporting. This is not a simple task—it involves significant effort to validate that the data received from the EMR matches the source records and is correctly mapped to the appropriate fields within the output files. Without this rigorous validation process, reporting errors and measure inaccuracies are almost inevitable.
• Data Blocking: Despite the Office of the National Coordinator for Health Information Technology’s (ONC’s) information blocking rules that went into effect in 2021, resistance persists. Many physicians still have trouble obtaining electronic health information from other providers or organizations, which could be a direct violation of Certified Electronic Health Record Technology (CEHRT) standards.
• Measure Version Control: Some EMRs have not committed to supporting the current versions of the MIPS CQM measures required for APP reporting. Many EMR vendors require additional customization costs to fully support the latest CMS quality measure specifications.

The experience of one mid-sized ACO provides a cautionary tale: despite receiving assurances from their primary EMR vendor about quality measures support, they discovered in Q3 2024 that critical data elements for three key measures were not being captured in the expected format. The resulting scramble to implement workarounds cost them substantial additional IT resources and consultant fees.

Strategic Approaches

ACOs must take a proactive stance in EMR coordination:

• Engage early with EMR vendors at a senior level—don't rely solely on technical contact
• Establish clear data specifications and performance expectations in writing
• Implement regular validation processes to confirm data accuracy
• Escalate non-cooperative EMRs to leadership and potentially to CMS

According to AJMC, ACOs that established formal governance processes for EMR data quality show fewer reporting errors than those without such frameworks.

Key Takeaway: Designate specific staff responsible for EMR coordination as a dedicated function, not an add-on responsibility. This role requires technical knowledge, relationship management skills, and a deep understanding of quality measures.

Lesson #4: Year-Round Workflows Are Essential

The legacy approach of initiating reporting processes in December is obsolete—the volume and complexity of reporting demand year-round attention and workflows.

Quarterly Workflow Imperatives

Best practices for implementing quarterly workflows include:

• Working on Q1-Q3 patients immediately upon receiving the patient lists
• Populating systems with numerator and denominator data throughout the year
• Establishing progressive completion targets (e.g., 30% by Q2, 60% by Q3)
• Conducting regular data completeness audits

Implementing these practices ensures a more manageable and efficient reporting process, minimizing last-minute challenges and errors.

Essential Tracking Elements

Effective year-round workflows require tracking several key data elements:

• Member attribution status
• Data presence verification for each required data source
• Quality measure eligibility determinations
• Exclusion and exception documentation
• Numerator compliance evidence

A systematic approach to tracking these elements throughout the year can dramatically reduce the end-of-year reporting burden. One large ACO reduced its Q4 manual abstraction requirements substantially by implementing progressive quarterly workflows.

Key Takeaway: Develop and implement quarterly workflows immediately. Aim to complete a majority of your reporting requirements before entering the final quarter of the performance year.

Critical Pitfalls and Pro Tips

Beyond the four primary lessons, several specific challenges have emerged as common pitfalls in APP reporting:

• ‍Missing Denominator Data: For non-assigned patients, claims data is often incomplete or unavailable, making denominator determination challenging. CMS data shows that denominator accuracy issues affect a significant portion of ACO quality measures in initial APP reporting.‍
• EMR Data Transmission Issues: Even when data format specifications are correct, some EMRs fail to transmit actual results. One ACO discovered that their EMR integration was passing patient identifiers but not the associated clinical values for key measures—a problem that went undetected for months.‍
• Vendor Cost Surprises: Many ACOs have encountered unexpected vendor charges for certain data outputs and workflows. Industry surveys show that many medical groups report paying additional fees to their EMR vendors specifically for quality reporting functionality.‍
• CEHRT Compliance Leverage: ACOs should remember that CEHRT requirements provide leverage with reluctant EMR vendors. Under ONC regulations, CEHRT must support quality measures reporting—a fact that can be leveraged in vendor negotiations.

Start Now With the Right Partner

The data from 2024 is conclusive: delayed planning directly correlates with lower quality scores. ACOs that waited until late in the year to begin APP reporting preparations consistently underperformed compared to those that adopted a proactive, year-round approach.

The urgency is real—and immediate action is essential. ACOs must quickly define their strategy around:

• Manual vs. automated data collection
• All patient, all payer eCQM vs. Medicare CQM vs. all-patient, all payer CQM reporting
• Staffing and resource allocation for quality reporting
• Technology investments for seamless data integration

It’s also important to understand that CMS requires ACOs to use a Qualified Registry vendor for quality reporting submissions—this may differ from your population health platform provider. Selecting a partner that offers both registry services and population health analytics delivers a strategic advantage, streamlining data integration, enhancing measure validation, and supporting performance improvement.

ACOs that partner with experienced population health analytics vendors are more likely to meet or exceed their quality goals than those managing the process alone. While the path forward may be complex, you don’t have to navigate it alone. Success depends on a knowledgeable partner and a well-defined strategy.

With the first quarterly files for 2025 reporting set to be released in late May, now is the critical moment to begin laying the groundwork for success in the evolving APP reporting landscape.

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