What Are the Biggest EHR Challenges Practices Face During CMS Submissions?

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The shift to electronic clinical quality measures has changed the game for Accountable Care Organizations. Starting in 2025, ACOs in the Medicare Shared Savings Program must submit eCQMs as their primary method for quality reporting, moving away from the legacy CMS Web Interface. This transition isn’t just a technical update. It fundamentally changes how ACOs collect, aggregate, and report quality data across their entire patient population, regardless of payer type.

Key Takeaways

  • ACOs must now report eCQMs for all patients meeting measure criteria, not just a sample of Medicare beneficiaries.
  • Data aggregation across multiple EHRs is the biggest technical hurdle most organizations face.
  • Early baseline measurement helps identify performance gaps before submission deadlines.
  • Provider education and workflow integration directly impact documentation accuracy and completeness.
  • Partnering with a qualified registry simplifies data submission and score optimization.

Understanding the eCQM Reporting Shift

The APM Performance Pathway now requires ACOs to submit clinical quality measures electronically, replacing the previous web-based approach. Under the old system, ACOs only needed to report on a sample of 248 Medicare patients. The new requirements expand that scope dramatically. Organizations must now analyze their entire patient population and report on all of their eligible patients across all payers.

CMS designed this transition to improve data interoperability and push ACOs toward digital processes that capture information in structured data fields. The Electronic Clinical Quality Measures Overview from CMS provides foundational guidance on how these measures work within certified EHR technology. 

For 2025, ACOs reported on measures covering diabetes management (HbA1c poor control), depression screening and follow-up, breast cancer screening, and controlling high blood pressure.  2026 is the same and will also include colorectal cancer screening as well. 

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Related: What is MIPS in Healthcare

Tackle Data Aggregation Head-On

The most significant challenge ACOs face with eCQM reporting is pulling data from multiple sources into a unified system. Many organizations operate with dozens of participating practices, each using different electronic health records. Some large ACOs work with 15 or more distinct EHR platforms, making data standardization incredibly complex.

Building a reliable aggregation workflow starts with understanding what data lives where. ACOs need to map out every TIN (Tax Identification Number) in their network and identify which EHR systems support each practice. From there, they can establish connections through APIs, sFTP transfers, or direct uploads to bring data into a central platform. Organizations dealing with ehr data integration challenges in mips reporting often find that working with a qualified registry streamlines this process significantly.

Data quality matters just as much as data collection. Research indicates that nearly 70% of ACOs rate their patient data quality as mixed or poor. Before submission, organizations should validate records to catch duplicates, verify patient matching across systems, and flag incomplete documentation.

Establish Performance Baselines Early

Waiting until the end of the reporting period to assess performance creates unnecessary risk. ACOs should run preliminary reports on their eCQM measures throughout the year to understand where they stand. This approach reveals which practices perform well and which need additional support.

For measures like HbA1c poor control, understanding your numerator and denominator populations helps pinpoint specific patient groups falling outside target ranges. The MIPS Quality Performance Category Requirements outline exactly how CMS calculates scores and what benchmarks apply to each measure. Tracking these numbers quarterly, or even monthly, gives clinical teams time to intervene before the reporting deadline arrives.

Real-time dashboards make this ongoing monitoring practical. When ACO leadership can see performance metrics at the organization, TIN, and individual provider level, they can direct resources where they’ll have the most impact.

Related: Maximizing MIPS Scores: Strategies to Improve Performance in 2025

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Invest in Provider Education and Workflow Integration

Technical infrastructure only gets an ACO halfway there. The clinicians documenting patient encounters need to understand what the measures require and how their EHR captures that information. 

Each certified EHR has specific workflows for entering data in the discrete fields that eCQM calculations pull from. If providers document in free text instead of structured fields, that information won’t count toward measure performance.

Training should focus on the practical, day-to-day actions that impact scores. For depression screening, providers need to know which screening tools the EHR supports and where to enter follow-up plans. 

For blood pressure control, staff should understand how readings flow into the system and what constitutes a qualifying measurement. These details vary by EHR platform, so education programs must be tailored to each practice’s specific technology.

The expansion to all-payer reporting also means specialists are now part of the equation. Dermatologists, cardiologists, and other specialists will be expected to contribute to measures traditionally seen as primary care responsibilities. ACOs should communicate clearly with these providers about their new role in quality performance.

Understand Submission Requirements and Timelines

Meeting Quality Payment Program Data Submission Requirements means understanding the technical specifications for eCQM files. ACOs can submit data in QRDA-I format, or through FHIR JSON for organizations using newer API-based approaches. Both formats require careful attention to data structure and validation rules.

Submission happens either through the Quality Payment Program portal, OR, via QCDR/Qualified Registry use of the CMS submission API, and ACOs should build in time for testing before final deadlines. Running test files through validation tools catches formatting errors and data issues that could cause rejection. Many qualified registries offer pre-submission review services to identify problems early.

CMS calculates quality scores by comparing measure performance against established benchmarks. Each measure can earn between 3 and 10 points based on how results stack up against historical performance data. 

Organizations meeting data completeness requirements and case minimums receive their full calculated score, while incomplete submissions may face reduced points or penalties.

Consider Partnering With a Qualified Registry

Managing eCQM reporting internally requires significant technical expertise, dedicated staff time, and ongoing investment in infrastructure. For many ACOs, partnering with a CMS-approved qualified registry makes more sense than building everything in-house.

A registry relationship provides access to purpose-built software for data aggregation, validation, and submission. Expert support teams help interpret measure specifications and troubleshoot issues throughout the reporting year. Perhaps most importantly, registries bring experience from working with multiple organizations, which means they’ve likely encountered and solved whatever challenges your ACO faces.

If your organization is preparing for eCQM reporting and wants to see how registry software works in practice, schedule a demo with Patient360 to explore their ACO reporting platform.

Conclusion

Success with eCQM reporting comes down to preparation, infrastructure, and engagement. ACOs that invest early in data aggregation, establish monitoring processes, educate their providers, and understand submission requirements position themselves for strong quality scores. 

The transition from web-based reporting demands more from organizations, but it also creates opportunities to build systems that improve care quality beyond just meeting CMS requirements. With the right approach and support, ACOs can turn eCQM reporting from a compliance burden into a foundation for better patient outcomes.