12 Mar Why MSSP ACOs Must Rethink Data Infrastructure for APP Quality Reporting

By Mark Coetzer, VP of Business Development at IMAT Solutions

The Medicare Shared Savings Program (MSSP) has shifted from the CMS Web Interface to electronic reporting under the Alternative Payment Model Performance Pathway. ACOs must now aggregate all payer data across their full patient population and submit quality measures electronically using QRDA III formats. This transition introduces new challenges around data completeness, EHR interoperability, patient matching, and reporting accuracy. As CMS continues aligning quality programs through 2028, ACOs will need stronger data infrastructure to maintain compliance, protect shared savings, and support future digital quality reporting.

A New Era of MSSP Quality Reporting

For years, Accountable Care Organizations (ACOs) participating in the Medicare Shared Savings Program relied on the CMS Web Interface to report quality measures through manual sampling and targeted chart abstraction. That approach allowed organizations to manage reporting across a limited subset of patients. That model has now changed.

CMS has retired the Web Interface and replaced it with mandatory electronic reporting under the Alternative Payment Model Performance Pathway (APP). Instead of sampling patients, ACOs must now report quality measures across their entire population using electronic clinical quality measures or MIPS clinical quality measures.

This shift requires organizations to aggregate, validate, and submit data electronically through standardized formats such as QRDA III, drawing from clinical information across multiple providers, systems, and payer sources.

For many ACOs, this transition has exposed a difficult reality, which is that clinical data is rarely report ready at the source.

The Data Infrastructure Challenge Facing ACOs

Most ACOs operate across networks of independent practices, hospitals, and specialists that rely on multiple electronic health record systems. These systems often capture clinical information in different formats, store data inconsistently, or lack the structured elements required for electronic quality reporting.

Only a small portion of ACOs operate within a single EHR environment. Many must aggregate data across several platforms, each with its own data structures, coding practices, and reporting capabilities.

As a result, organizations frequently encounter missing data elements in CCDAs or QRDA files, limited interoperability across systems, inconsistent coding across clinical sites, and critical information trapped in unstructured documentation.

When reporting relied on patient sampling, these issues could sometimes be resolved through manual review. In the new electronic reporting environment, those workarounds disappear. ACOs must now depend entirely on the integrity and completeness of their underlying data.

Full Population Reporting Raises the Stakes

The transition to APP reporting also expands the scale of quality measurement. Instead of reporting on a sample, ACOs must now include all eligible patients in their reporting population. That population may include hundreds of thousands or even millions of individuals when all payer data sources are considered. This introduces new operational complexity.

Patient records must be aggregated from multiple systems and matched accurately across sources. Duplicate records must be resolved without excluding eligible patients. Data completeness thresholds must be met across the entire denominator population. Performance rates must be calculated based on the full clinical dataset rather than partial samples.

For many organizations, these requirements create significant technical and operational strain. Without a unified data foundation, teams often resort to fragmented spreadsheets, manual reconciliation, and late stage troubleshooting to prepare submissions. These approaches increase risk and reduce confidence in reported results.

Looking Toward the CMS Quality Framework Through 2028

The shift to electronic reporting is part of a broader transformation in CMS quality measurement. Over the next several years, CMS is working toward a unified foundation of quality measures that will align reporting requirements across multiple Medicare programs. The goal is to simplify reporting while ensuring consistent performance measurement across the healthcare system.

The transition to electronic reporting is already underway. In the coming years, CMS will increase its focus on social determinants of health data and health equity benchmarks. Looking toward 2028, a key objective is the closer alignment of quality measures across federal programs, driven by the use of standardized digital clinical data and the integration of FHIR and CQL standards into the digital quality measurement (dQM) framework.

For ACOs, this means quality reporting will increasingly depend on reliable, interoperable data that can support multiple regulatory frameworks at once. Organizations that treat electronic reporting as a one-time compliance task may find themselves unprepared for the next phase of digital measurement.

Health Equity and REACH Readiness

Health equity and social determinants of health reporting are becoming central priorities in value-based care.

CMS programs increasingly require organizations to stratify quality performance across different patient populations, including race, ethnicity, geography, and socioeconomic factors, to identify disparities in care. For ACOs, this means capturing SDOH data, integrating it with clinical and claims information, and analyzing performance across demographic groups.

IMAT enables ACOs to stratify quality metrics, identify care gaps affecting vulnerable populations, and align reporting with emerging CMS health equity initiatives.

Why Many ACOs Struggle with Electronic Reporting

The difficulty of APP reporting does not stem from measure logic alone. Most quality teams already understand the clinical guidelines behind the measures they report. The challenge lies in the data itself.

Clinical information may originate from different EHR systems, claims feeds, laboratories, pharmacies, and health information exchanges. Each source may use different coding practices, data formats, and update schedules. Without normalization and validation, these differences can create inconsistencies that affect measure accuracy.

Even when data exists, it may not appear in the expected fields required for QRDA reporting. Documentation gaps may prevent numerator credit. Incomplete diagnosis capture may affect risk adjustment and benchmark comparisons.

When these issues surface late in the reporting cycle, ACOs may have little time to correct them before submission deadlines. A stronger data foundation allows organizations to identify and resolve these problems earlier in the process.

How IMAT Helps ACOs Navigate the Reporting Evolution

IMAT Solutions was designed to address the data challenges that modern value-based care programs expose.

Our IMAT Intelligence platform aggregates all required clinical data across participating providers. These data streams are normalized into a standardized structure aligned with CMS reporting requirements, creating a unified source of truth for quality measurement.

Once data is aggregated, IMAT Intelligence enables organizations to validate and analyze performance before submission. ACOs gain visibility into patient level care gaps, provider level performance trends, and documentation issues that may affect measure accuracy. Real time dashboards allow teams to monitor numerator and denominator status throughout the performance year rather than waiting until submission.

Our platform also supports patient identity resolution through enterprise level patient matching and deduplication. This ensures that the eligible population for reporting includes all relevant patients without inflating counts through duplicate records.

When submission time arrives, IMAT generates the required QRDA III quality reports for CMS reporting.

IMAT helps ACOs aggregate, normalize, and validate clinical data across multiple systems to support accurate MSSP reporting, stronger performance insights, and greater confidence at submission time.

Learn how IMAT Intelligence can help your organization build a unified data foundation for APP reporting and the next generation of digital quality measurement. Contact IMAT Solutions today to start the conversation.

About the Author
Mark Coetzer is VP of Business Development at IMAT Solutions, with more than 30 years of technology experience and a decade dedicated to healthcare. He brings deep expertise in clinical data integration, interoperability, and population health, and is passionate about helping organizations build trusted data foundations for better care and smarter outcomes.

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