eCQM Reporting for Medicare ACOs: Beyond the CMS Web Interface

The post-Web-Interface reality

For close to a decade, MSSP ACOs had a reasonably forgiving path to quality reporting: pick a sample of 248 Medicare-assigned patients from a CMS-curated list, fill in the data, submit through the Web Interface.

The Centers for Medicare & Medicaid Services (CMS) retired the Web Interface at the end of the 2024 performance year, and every ACO in the Medicare Shared Savings Program is now reporting through the APM Performance Pathway or its expanded successor, APP Plus.

The Web Interface let ACOs report on 248 sampled patients. APP Plus asks them to report on everyone.

ACOs went from sample-based reporting on a few hundred patients to all-payer reporting across their full assigned population, with a 70% data completeness threshold and quality measures calculated from actual clinical data rather than chart-abstracted samples. For ACOs that had built quality reporting workflows around the old model, the transition has been a multi-year scramble.

The three reporting paths

Under APP Plus, ACOs choose one of three collection types for the quality measures. The choice has significant operational consequences:

eCQMs and MIPS CQMs cover all payers. Good for benchmarking, but it means aggregating data on every patient across every participating practice. Medicare CQMs narrow the population to Medicare FFS beneficiaries only, which are exactly the patients CMS is measuring the ACO on, at the cost of forfeiting the eCQM/MIPS CQM reporting incentive.

Why multi-EHR data aggregation is the real challenge

This is the part the original 2024 paper got most right, and it’s only become more relevant since: the technical difficulty of ACO reporting is not measure calculation. It’s data aggregation.

A typical MSSP ACO includes multiple Tax Identification Numbers (TINs) — independent practices, often hospital-affiliated, sometimes Federally Qualified Health Centers, occasionally a Rural Health Clinic or two. Each runs its own EHR. Each has its own definition of what “patient” means, its own coding habits, its own data quality. To report APP Plus quality measures, the ACO has to:

• Collect structured clinical data from every participating TIN, ideally as QRDA Category I or FHIR resources
• Deduplicate patients who appear across multiple practices (which is half the assigned population in some ACOs)
• Normalize coding inconsistencies across EHR vendors — value sets, units, problem list conventions
• Calculate measures across the aggregated dataset, not per-practice
• Validate that the result meets the 70% data completeness threshold across the full assigned population

None of this is theoretical. CMS introduced a “Complex Organization Adjustment” beginning with CY 2025 specifically because Virtual Groups and ACOs faced material disadvantages in eCQM reporting compared to single-EHR practices. The adjustment helps with scoring. It doesn’t eliminate the underlying technical problem.

The APP Plus measure set is growing

APP Plus isn’t static. CMS has laid out a multi-year expansion that increases the reporting burden every year through PY 2028:

Year	Measures	Total
PY 2025	4 eCQMs/MIPS CQMs/Medicare CQMs + 1 admin claims + CAHPS for MIPS	6
PY 2026 (current)	5 quality measures + 2 admin claims + CAHPS · Colorectal cancer screening added. Last year for MIPS CQMs.	8
PY 2027	Substance use disorder measures phase in	9
PY 2028	Social determinants, immunizations, and additional measures	11

The implication for ACOs is straightforward: any infrastructure investment made today needs to support not the PY 2026 measure set but the PY 2028 one. Shortcuts that get you through this year’s submission will compound into next year’s emergencies. For more on the specific measures being phased in, see our blog post on the APP Plus quality measure set.

Bulk FHIR: the long-term foundation

The 2024 paper called FHIR “a pivotal component of long-term solutions”. CMS, ASTP/ONC, and the major standards bodies have converged on FHIR R4 with USCDI v3 as the foundation for the next generation of quality and interoperability reporting.

For ACOs, the relevant pieces are:

• FHIR Bulk Data Access — the standardized mechanism for pulling patient populations from participating EHRs, replacing per-patient API calls that don’t scale to ACO-sized populations
• USCDI v3 data elements — the standardized clinical data set that quality measure calculations are increasingly written against
• FHIR-based eCQMs — the gradual transition from QRDA-based calculation to FHIR-native logic, with HL7’s Da Vinci and CodeX accelerators leading the standards work

ACOs that invest in FHIR-capable data infrastructure now won’t have to re-platform when FHIR-native quality reporting becomes the default path. Those that wait will be re-platforming under deadline pressure.

A note on UDS overlap for FQHC-led ACOs

ACOs that include Federally Qualified Health Centers face an additional reporting layer: HRSA’s Uniform Data System (UDS), which has its own quality measure requirements and is moving toward FHIR-based patient-level submission through the emerging UDS+ framework. The good news is that HRSA has aligned UDS quality measures with eCQM logic. The data infrastructure built for APP Plus can do double duty for UDS, assuming the visit logic and patient identifiers reconcile cleanly. We cover this in detail in our UDS Reporting Guide for FQHCs.

About the DHIT ACO solution

Dynamic Health IT, Inc. (DHIT) has provided quality measure calculation and reporting software since 1999. Our CQMsolution platform is ONC-certified for eCQM calculation, and our Dynamic FHIR API handles the data ingestion side — FHIR Bulk, QRDA Category I, and FHIR resources from different EHRs — feeding into a DataStore designed to aggregate, deduplicate, and calculate measures across multi-TIN ACO populations.

ACOs need exactly this kind of multi-EHR infrastructure, and that’s why Dynamic Health IT built an end-to-end ACO reporting solution combining our CQMsolution quality measure engine, the Dynamic FHIR API, and an ACO performance dashboard.

For a walkthrough of the platform, or a working session on your ACO’s specific data aggregation challenges, get in touch.