2025 DIY Guide to MSSP ACO eCQM Reporting: From Clinical Data Chaos to Submission Success

Is your Medicare Shared Savings Program (MSSP) ACO ready to tackle the complex world of electronic Clinical Quality Measures (eCQM) reporting? While some organizations consider building their own internal reporting capabilities, the reality is that aggregating data from multiple EHRs, ensuring measure compliance, and preparing submission-ready files requires significant expertise and coordination that many underestimate. 

eCQM reporting for MSSP ACOs isn’t just a technical checkbox, it’s a high-stakes, data-driven operation that directly impacts your quality scores and shared savings potential. This guide walks you through the essential steps: acquiring and validating data, identifying critical gaps, de-duplicating patients, monitoring quality performance, and generating compliant submission files. 

2025’s eCQM Landscape: What’s at Stake 

For performance year 2025, MSSP ACOs must report four specific eCQM/MIPS CQM measures as part of the APP Plus quality measure set: 

1. Diabetes: Hemoglobin A1c (HbA1c) Poor Control 
   The percentage of patients age 18–75 with diabetes whose most recent HbA1c is greater than 9.0%.
2.  Preventive Care and Screening: Depression Screening + Follow-Up Plan
   The percentage of patients age 12 or older who are screened for depression and, if positive, have a documented follow-up plan.
3. Controlling High Blood Pressure
   The percentage of patients age 18–85 with diagnosed hypertension whose blood pressure is controlled (meaning less than 140/90 mmHg).
4. Breast Cancer Screening
   The percentage of women age 50–74 who received a mammogram every one to two years. 

The requirements will continue expanding, with additional eCQM/MIPS CQM measures phasing into the APP Plus set, including colorectal cancer screening (2026), substance use disorder measures (2027), and social determinants, immunizations, and other measures through 2028. 

So, what are some steps you can take?  

Step 1: Acquire Comprehensive Data Across All Practices 

Success begins with collecting structured clinical data from every provider (NPI) participating in your ACO. Given that practices often use different EHR vendors, there are usually inconsistencies when it comes to the format and completeness, which will require strategic coordination. 

Focus your data acquisition efforts on: 

• EHRs: All participating TINs must have a CEHRT version of their EHR for eCQM submission. Request QRDA-1 files where possible, as these provide the most standardized format. 
• Clinical Data Repositories (CDRs): Leverage existing clinical data aggregation solutions to supplement clinical data across organizations. 
• Alternative formats: When QRDA-1 isn’t available or reliable, request FHIR, CCDA, or flat-file extracts (CSV, JSON) to ensure comprehensive data capture. 

Early engagement with EHR vendors is critical to understand their capabilities, pricing structures, and limitations around extracting the right clinical data for CMS measures. 

Step 2: Identify and Fix Critical Quality Gaps 

Even structured data can be incomplete, and gaps can significantly impact your performance scores or make patients ineligible for measure inclusion. Comprehensive validation ensures you’re working with accurate and compliant information. 

Essential validation tasks include: 

Chart Review: While the volume of qualifying patient encounters will be substantially larger than previous years, select a representative sample of patients for each provider to ensure documentation accuracy is reflected in data extracts. Work closely with clinical teams to ensure documentation occurs in structured fields, not just narrative notes. 

Patient Attribution: Cross-reference your ACO-assigned patient list from CMS against EHR and billing data to ensure complete coverage and accurate attribution. 

Common issues that require attention: 

• Missing vital signs such as blood pressure readings 
• Tobacco use not recorded in structured EHR fields 
• External lab results never entered into the primary EHR system 
• Incomplete or inconsistent diagnostic coding 

Step 3: Aggregate Multi-EHR Data into a Unified Repository 

Your ACO needs to consolidate data from all participating practices into a central, standardized repository. Since EHR formats vary significantly, focus on creating uniform data structures using proven approaches: 

Technical approaches for data aggregation: 

• Third-party data platforms can automate aggregation and normalization processes, reducing manual effort and technical complexity. 
• Customize ETL pipelines using tools like Apache NiFi, Talend, or scripting languages (Python, SQL) for organizations with dedicated technical resources. 
• Common Data Models (CDMs) such as OMOP or FHIR can standardize disparate inputs and create interoperable data structures. 

Your goal is to create a comprehensive, longitudinal patient record that spans all contributing systems while maintaining data integrity and clinical context. 

Step 4: De-Duplicate and Link Patient Records 

Multiple providers within your ACO may treat the same patient, and duplicates can significantly skew numerators and denominators, leading to inaccurate quality scores that impact your shared savings potential. 

Address duplication using proven methodologies: 

• Master Patient Index (MPI) systems or probabilistic record linkage based on patient attributes such as name, date of birth, gender, address, and phone number. 
• Unique patient identifiers assigned consistently across all systems to prevent future duplication. 
• Manual review processes for edge cases with conflicting or overlapping records that automated systems cannot resolve. 

Step 5: Continually Monitor ACO Quality Performance 

Don’t wait until submission time to assess your performance. Building a comprehensive dashboard for continuous monitoring across the ACO provides critical insights for timely interventions. 

Include these essential components: 

• Measure-level tracking: Monitor denominator inclusion, numerator compliance, and exclusions for each quality measure. 
• Provider and TIN-level analytics: Identify high- and low-performing practices and individual providers to target improvement efforts. 
• Time-based trending: Track changes monthly or quarterly to inform targeted interventions and measure improvement over time. 

This ongoing monitoring approach allows course corrections throughout the performance year rather than discovering issues at submission time. 

Step 6: Generate and Submit QRDA-III and JSON File  

After validating and aggregating your performance data, generate final submission files in one of two CMS-accepted formats: 

1. QRDA-III (XML): CMS’s established submission format for aggregate data, widely supported by existing systems and vendors. 
2. FHIR JSON: A modern, API-based format aligned with CMS Digital Quality Measurement (dQM) initiatives, representing the future direction of quality reporting. 

For QRDA-III file generation: 

• Utilize certified eCQM vendor tools (like MRO) for streamlined compliant file creation. 
• Develop custom scripts to convert cleaned data to QRDA-III XML using libraries like lxml (Python) or libxml2. 

Submission options: 

• Upload QRDA-III files directly to the Quality Payment Program (QPP) portal. 
• Submit JSON files through FHIR APIs if your ACO has implemented direct reporting capabilities. 

 Should Your MSSP ACO Build or Partner for eCQM Reporting? 

While building your own eCQM reporting pipeline offers control and customization, it’s also a complex, resource-intensive endeavor requiring technical expertise, dedicated infrastructure, and constant regulatory vigilance. Success depends on your organization’s ability to collaborate effectively with participating practices, standardize data across diverse systems, diligently validate and match patients, and maintain ongoing performance monitoring with timely course corrections. 

For many ACOs, the strategic path forward involves partnering with an experienced vendor like MRO, who specializes in healthcare data aggregation, quality reporting, and compliance. With our deep understanding of eCQMs, EHR integrations, and CMS submission requirements, MRO helps streamline the entire process, from data extraction and validation to QRDA file creation and submission, allowing your organization to focus on improving care and performance rather than wrestling with technical complexities. Our comprehensive platform supports all reporting methods and combines data from different sources to help you submit your highest scores for maximum shared savings potential. 

Get Empowered to Navigate 2025’s eCQM Reporting

Whether your ACO chooses to develop internal capabilities or partner with experienced vendors, the key to success lies in early planning, comprehensive data management, and continuous performance monitoring. The stakes are high, but with the right approach and resources, your organization can turn eCQM reporting from a compliance burden into a strategic advantage for improving patient care and maximizing shared savings. 

Contact MRO today to learn how our comprehensive eCQM reporting solutions can help your ACO achieve optimal performance while maintaining focus on what matters most – delivering exceptional patient care.