Why EHRs Fall Short for CMS Care Management Compliance

In the face of growing calls for value-based care, reduced reimbursement, and increasing costs, providers are launching care management programs to help counteract these pressures.

While many providers assume their electronic health record (EHR) can support these initiatives, the reality is more complicated.

EHRs were initially built for billing and documentation, rather than for managing complex care coordination and patient-centered care planning. Even with bolt-on modules and plug-in feature sets, clients say their EHR can’t fulfill the role that dedicated care management software can.

When providers attempt to repurpose their EHR for care management operations, they often come to us after experiencing missed billing opportunities, delayed or denied reimbursement, or when facing a program audit.

In this blog, we’ll explore the eight reasons why EHRs are a risky option for CMS care management compliance. Plus, we’ll demonstrate why ThoroughCare not only fills EHR gaps but delivers far more value, efficiency, and compliance.

EHR vs. ThoroughCare: Feature comparison for CMS care management programs

Figure 1  below highlights how many EHRs handle specific features and Medicare requirements when compared to ThoroughCare. Keep reading to learn how EHR shortfalls necessitate a complementary care management solution.

Figure 1: How does ThoroughCare compare to a typical electronic health record?

EHR shortfall #1: EHRs lack workflows built for care management

At their core, most EHRs are designed to capture clinical encounters, support diagnosis and treatment workflows, and handle billing for in-office, face-to-face care. But CMS care management program workflows require a completely different approach—one centered around non-face-to-face, ongoing patient engagement.

Medicare care management programs require providers to:

• Identify eligible patients
• Secure and document consent
• Build and regularly update care plans
• Track care coordination across providers and disciplines
• Log billable time accurately
• Report services provided each month

Unfortunately, most EHR systems do not offer native workflows for these tasks. 

Providers are left trying to manage compliance using manual workarounds, spreadsheets, or disjointed notes, which is both inefficient and risky.

EHR shortfall #2: Time tracking for non-face-to-face care is weak or missing

One of the most critical requirements in CMS care management billing is documenting the time spent each month on non-face-to-face services. For example, both Chronic Care Management (CCM) and Principal Care Management (PCM) require a minimum of 20 minutes per month of clinical staff time directed by a provider.

Other Medicare programs require CPT codes tied to time tracking as well, including:

• Remote Patient Monitoring (RPM)
• Behavioral Health Integration (BHI)
• Annual Wellness Visits (AWV)
• Advance Care Planning (ACP)

Yet, most EHRs don’t provide any structured or automated way to meet time tracking requirements, including:

• Log time for non-visit-based tasks like care coordination, medication reconciliation, or phone calls
• Associate time entries with the correct CPT codes
• Verify compliance with CMS time thresholds before billing

These gaps create two challenges. 

First, providers risk under-documenting and potentially losing revenue. Second, in the event of a Medicare audit, a lack of verifiable time tracking can lead to recoupments or penalties.

EHR shortfall #3: Inadequate consent and enrollment tracking

CMS requires that patients consent to enrollment in care management programs. 

Consent may be verbal or written, but must be documented clearly in the medical record. Providers must also track whether patients remain enrolled, opt out, or need to re-consent after changes in coverage or care.

Unfortunately, EHRs typically don’t have built-in tools for this purpose, including:

• Capturing and storing consent documentation
• Flagging whether a patient is actively enrolled
• Reminding staff when re-consent is needed

As a result, practices may fail to document consent or re-consent patients on time—both of which could jeopardize compliance and billing.

EHR shortfall #4: Poor support for CMS-compliant care plans

CMS requires that patients in care management programs have a comprehensive, dynamic care plan that is regularly reviewed and updated. These care plans must include the following elements:

• Patient-centered goals
• Identified problems and diagnoses
• Planned interventions
• Care team roles
• Measurable outcomes

Most EHRs are structured for visit-based documentation rather than longitudinal care planning. 

Care plan, if offered, are often templates that providers must create from scratch. They tend to remain as static documents that are buried in the record and rarely updated. This makes it challenging to meet CMS expectations for active care plan management. It’s even more difficult to demonstrate compliance during audits.

EHR shortfall #5: Incomplete documentation of required services

CMS care management programs often include required services that aren’t directly tied to individual encounters, including:

• Medication reconciliation
• Use of certified EHR technology
• 24/7 access to care team support
• Ongoing communication between patient and care team

These services must be documented, even though they may not generate their own billable codes. EHRs frequently lack fields or workflows to capture these actions in a structured and retrievable way, making it difficult to prove that all CMS billing conditions were met.

EHR shortfall #6: No alerts or automation for compliance deadlines

Care management programs are not one-and-done activities. Providers must track recurring monthly touchpoints, care plan reviews, and other time-sensitive actions.

Yet most EHRs fall short because they lack features, such as:

• Automated and prioritized worklists and reminders to follow up with a patient
• Alerts for missed monthly services
• Dashboards for tracking care delivery status across patient panels

This can result in missed monthly contacts (and lost billing opportunities), or worse, accidental overbilling when services were not provided as required.

EHR shortfall #7: Inadequate reporting and audit support

When CMS audits a care management program, they expect providers to produce detailed, structured reports showing key data, including:

• Which patients received services each month
• What care management services were delivered
• How much time was spent and if the minimum time was achieved
• Who delivered the care and who signed off and oversaw that care
• Whether the required elements, like consent and care planning, were documented

EHRs often can’t generate these reports without custom queries, IT support, or third-party tools. 

This creates a serious bottleneck when preparing for audits or efficiently managing a scalable program. Providers who rely solely on EHR data may struggle to demonstrate compliance.

EHR shortfall #8: Poor interoperability with external care teams

CMS care management purposefully involves team-based care across providers, clinics, hospitals, and even community resources. To meet CMS expectations for coordinated care, providers need to share care plans, document external communications, and track referrals.

Here, again, most EHRs are closed systems with limited ability to interface with outside providers, especially those on different platforms. This undermines the “coordination” aspect of care management, creating documentation gaps and compliance risks.

ThoroughCare provides comprehensive software for care management

ThoroughCare supports healthcare organizations with effective, evidence-based care management. 

Our team of in-house clinical experts, technologists, and industry specialists helps providers optimize their programs through People, Process, and Technology. Our software was purpose-built to support the unique workflows, communication, and coordination aspects of care management programs, offering:

• Automated patient eligibility and consent tracking
• Built-in time logs and billing compliance oversight
• Evidence-based, guided clinical and social risk assessments
• Structured care plan templates aligned with CMS guidelines
• Task management automation and reminders for recurring care
• AI-driven call management and communication
• Centralized dashboards, worklists, and reports that track performance and highlight gaps
• Integrated workflow and features that make CMS compliance simpler

While EHRs are essential for clinical documentation, they often lack specialized functionality for CMS compliance for care management programs. ThoroughCare fills this gap by providing purpose-built tools that streamline workflows, improve documentation, and support billing.

Rather than relying on patchwork documentation, inadequate EHR functionality, or risky manual workarounds, providers who use ThoroughCare experience new capacity and capabilities. 

We help reduce administrative burdens, improve patient care, maximize reimbursements, as well as support better compliance.