Medication Therapy Management (MTM) Software: Complete Guide for Clinical Pharmacies 2026

Medication Therapy Management (MTM) represents one of the most significant revenue and patient care opportunities for pharmacies in 2026. With Medicare Part D MTM programs, commercial payer initiatives, and expanded clinical pharmacy services, MTM software platforms have become essential tools for delivering, documenting, and billing comprehensive medication reviews. This guide covers everything you need to know about MTM software, CMS requirements, top platforms, and strategies for building a profitable clinical pharmacy practice.

What is Medication Therapy Management (MTM)?

Medication Therapy Management is a distinct service or group of services provided by pharmacists to optimize therapeutic outcomes for individual patients. MTM services are independent of, but can occur in conjunction with, the provision of a medication product.

Core MTM Services

Comprehensive Medication Review (CMR):

• Systematic review of all patient medications (prescription, OTC, herbals, supplements)
• Identification of medication-related problems
• Development of Personal Medication Record (PMR)
• Creation of Medication Action Plan (MAP)

Targeted Medication Reviews (TMRs):

• Focused interventions for specific drug therapy problems
• Adherence assessments and interventions
• Cost-saving opportunities identification

Additional Clinical Services:

• Immunization coordination and administration
• Disease state management (diabetes, hypertension, asthma)
• Medication synchronization programs
• Transitions of care services

MTM Market Size and Growth

The medication therapy management market is experiencing robust growth driven by:

• Aging Population: 77 million baby boomers requiring complex medication regimens
• Chronic Disease Prevalence: 60% of adults have at least one chronic condition
• Healthcare Cost Pressures: Medication-related problems cost $528 billion annually
• Regulatory Support: CMS and state-level recognition of pharmacist provider status
• Payer Expansion: Commercial insurers launching MTM programs beyond Medicare

2026 CMS MTM Program Requirements

For 2026, Medicare Part D MTM programs have specific eligibility criteria:

Patient Eligibility Criteria

Patients qualify for MTM services if they meet ALL three criteria:

1. Multiple Chronic Conditions: At least three chronic diseases including:

• Diabetes mellitus
• Chronic heart failure
• Hypertension
• Dyslipidemia
• Chronic obstructive pulmonary disease (COPD)
• Asthma
• End-stage renal disease (ESRD)
• Mental health conditions

2. Multiple Part D Drugs: Taking 8 or more covered Part D maintenance medications concurrently

3. Cost Threshold: Likely to incur annual Part D drug costs of $1,276 or more (2026 threshold based on average cost of eight generic drugs)

MTM Program Deliverables

CMS requires Part D plans to provide:

• Annual Comprehensive Medication Review (CMR): In-person, telehealth, or telephonic review
• Quarterly Targeted Medication Reviews: Four times per year minimum
• Personal Medication Record (PMR): Comprehensive list of all medications
• Medication Action Plan (MAP): Patient-friendly summary of recommendations
• Standardized Format: CMS-required template for PMR and MAP
• Intervention Documentation: Outcomes and recommendations tracking

Leading MTM Software Platforms for 2026

1. OutcomesONE by Outcomes

OutcomesONE provides a unified ecosystem managing everything from dispensing to medication therapy management to patient engagement.

Key Features:

• Integrated platform connecting pharmacies, payers, and pharma programs
• CMS-compliant CMR and TMR workflows
• Electronic health record (EHR) integration
• Patient portal for MAP and PMR access
• Automated eligibility identification
• Billing and claims submission
• Clinical decision support tools

Ideal For: Pharmacies seeking comprehensive platform with payer connections

2. Aprexis

Aprexis offers an integrated MTM software platform with customizable clinical programs focusing on lifestyle medicine, disease management, and patient-centered pharmacy care.

Key Features:

• Cloud-based platform accessible anywhere
• Telepharmacy and telehealth capabilities
• Clinical program templates (diabetes, hypertension, asthma)
• Patient communication tools (SMS, email, portal)
• Outcomes tracking and reporting
• Multi-pharmacy network support
• Payer contract management

Ideal For: Independent pharmacies and pharmacy networks building MTM programs

3. DocStation

DocStation redefines MTM pharmacy services with a state-of-the-art electronic health record (EHR) designed specifically for pharmacists.

Key Features:

• Comprehensive pharmacy EHR
• CMS MTM program participation tools
• CPT code billing for MTM services
• Patient encounter documentation
• SOAP note templates
• E-prescribing integration
• Lab result integration
• Chronic disease management modules

Ideal For: Pharmacies billing MTM services under CPT codes or seeking full EHR functionality

4. Mirixa (Tabula Rasa HealthCare)

Mirixa provides comprehensive medication risk management and MTM services.

Key Features:

• MedWise medication safety platform
• Pharmacogenomics integration
• Multi-drug interaction analysis
• Deprescribing recommendations
• Risk scoring algorithms
• Population health management
• Payer network connections

Ideal For: Pharmacies focused on high-risk patient management and medication optimization

5. PharmaPOS Clinical Module

PharmaPOS offers integrated clinical pharmacy services within the pharmacy management platform.

Key Features:

• MTM service documentation
• Patient medication records
• Clinical intervention tracking
• Billing integration for clinical services
• One-time licensing with no monthly fees
• Offline capability for rural areas
• Integration with dispensing workflow

Ideal For: Pharmacies seeking integrated MTM within existing pharmacy management system

Essential MTM Software Features

When evaluating MTM software platforms, prioritize these capabilities:

1. Patient Eligibility Identification

Automated Eligibility Screening:

• Integration with pharmacy dispensing system
• Real-time identification of MTM-eligible patients
• Payer-specific criteria application
• Outreach prioritization based on risk scores

Multi-Source Data Integration:

• Prescription claims data
• Medical claims (if available)
• Lab values
• Diagnosis codes

2. Comprehensive Medication Review Tools

Clinical Decision Support:

• Drug-drug interaction checking
• Drug-disease contraindication alerts
• Duplicate therapy identification
• Therapeutic alternatives suggestions
• Adherence scoring
• Cost-saving opportunities

Documentation Templates:

• CMS-compliant CMR documentation
• SOAP note formats
• Custom clinical protocol templates
• Voice-to-text capability
• Mobile documentation apps

3. Patient Communication and Engagement

Multi-Channel Outreach:

• Automated appointment reminders (SMS, email, phone)
• Patient portals for MAP/PMR access
• Secure messaging
• Video conferencing for telehealth MTM
• Mobile app for patient engagement

Educational Materials:

• Medication-specific education
• Disease state management resources
• Multi-language support
• Health literacy-appropriate content

4. Billing and Claims Management

Revenue Cycle Management:

• CMS MTM claims submission
• CPT code billing (99605, 99606, 99607)
• Commercial payer billing
• Cash pay invoicing
• Payment posting and reconciliation
• Denial management

Reimbursement Tracking:

• Per-service revenue tracking
• Payer mix analysis
• Pharmacist productivity metrics
• ROI calculation

5. Outcomes Tracking and Reporting

Clinical Outcomes:

• Medication-related problem identification and resolution
• Clinical parameter improvements (A1c, blood pressure, cholesterol)
• Medication adherence rates
• Emergency department visit reductions
• Hospitalization prevention

Operational Metrics:

• CMRs and TMRs completed
• Completion rates by payer
• Patient satisfaction scores
• Staff productivity
• Revenue per MTM encounter

6. Interoperability and Integration

EHR/EMR Integration:

• Read patient medical history
• Access lab values
• Review diagnosis codes
• Send recommendations to prescribers
• E-prescribing for protocol-based care

Pharmacy System Integration:

• Single sign-on from dispensing system
• Medication history access
• Refill synchronization
• Point-of-sale integration for cash MTM services

Building a Profitable MTM Practice

Revenue Streams for MTM Services

1. Medicare Part D MTM Programs

• Average reimbursement: $50-$75 per CMR
• Volume: Based on eligible patient population
• Payment timeline: Typically quarterly

2. CPT Code Billing

• 99605: Initial 15 minutes, face-to-face
• 99606: Initial 15 minutes, non-face-to-face
• 99607: Each additional 15 minutes
• Reimbursement varies by payer ($20-$60 per 15 minutes)

3. Commercial Payer Contracts

• Employer-sponsored programs
• Health plan MTM initiatives
• ACO and value-based contracts
• Average: $40-$100 per encounter

4. Cash-Pay MTM Services

• Annual medication review: $75-$150
• Focused consultations: $30-$75
• Disease management programs: $50-$100/month

5. Manufacturer-Sponsored Programs

• Patient support services
• Adherence programs
• Specialty medication management
• Typical payment: $25-$75 per intervention

MTM Practice Development Strategy

Phase 1: Foundation (Months 1-3)

Technology Implementation:

• Select and implement MTM software
• Integrate with pharmacy management system
• Train staff on platform
• Configure documentation templates

Payer Enrollment:

• Enroll in Medicare Part D MTM networks
• Obtain NPI and NCPDP numbers
• Complete payer credentialing
• Set up billing processes

Workflow Development:

• Create standard operating procedures
• Define staff roles and responsibilities
• Establish patient scheduling process
• Develop documentation standards

Phase 2: Launch (Months 3-6)

Patient Outreach:

• Identify eligible patients through software
• Launch outreach campaigns (phone, SMS, in-person)
• Schedule initial CMRs
• Begin service delivery

Staff Training:

• Clinical skills development
• Motivational interviewing techniques
• Documentation best practices
• Billing and coding education

Quality Assurance:

• Review documentation for completeness
• Monitor completion rates
• Track outcomes
• Adjust workflows based on feedback

Phase 3: Growth (Months 6-12)

Expand Services:

• Add disease state management programs
• Implement medication synchronization
• Launch specialty pharmacy MTM
• Develop transitions of care services

Enhance Reimbursement:

• Contract with commercial payers
• Implement CPT code billing
• Develop cash-pay service menu
• Pursue manufacturer programs

Scale Operations:

• Hire dedicated MTM pharmacists
• Expand appointment availability
• Optimize scheduling efficiency
• Leverage telepharmacy for access

Phase 4: Optimization (Year 2+)

Data-Driven Improvement:

• Analyze outcomes data
• Identify high-impact interventions
• Refine patient selection criteria
• Optimize pharmacist productivity

Advanced Services:

• Pharmacogenomics testing
• Continuous glucose monitoring
• Point-of-care testing (A1c, lipids, INR)
• Collaborative practice agreements

MTM Documentation Best Practices

Comprehensive Medication Review Documentation

Required Elements:

1. Patient Demographics: Name, DOB, contact information

2. Medication List: All prescription, OTC, herbals, supplements

3. Allergies and Adverse Reactions: Complete history

4. Medical Conditions: Current diagnoses

5. Medication-Related Problems Identified:

   • Indication without medication
   • Medication without indication
   • Ineffective medication
   • Dosage too low
   • Adverse drug reaction
   • Dosage too high
   • Non-adherence
   • Drug interaction
   • Duplicate therapy
   • Cost-related issues

6. Interventions and Recommendations:

   • Specific actions taken
   • Provider communications
   • Patient education provided
   • Referrals made

7. Follow-Up Plan: Next steps and timeline

8. Personal Medication Record (PMR): CMS-required format

9. Medication Action Plan (MAP): Patient-friendly summary

SOAP Note Template for MTM

Subjective:

• Chief complaint/reason for visit
• Patient-reported symptoms
• Medication-taking behaviors
• Barriers to adherence

Objective:

• Vital signs (if obtained)
• Lab values (if available)
• Medication list verification
• Prescription fill history

Assessment:

• Medication-related problems identified
• Clinical status evaluation
• Risk assessment

Plan:

• Recommendations for prescribers
• Patient education provided
• Lifestyle modifications discussed
• Follow-up schedule
• Measurable goals established

Overcoming Common MTM Implementation Challenges

Challenge 1: Low Patient Participation Rates

Problem: Eligible patients don't schedule or complete MTM appointments

Solutions:

• Personal Outreach: Phone calls more effective than letters
• Scheduling at Pickup: Offer MTM when patient picks up prescription
• Incentives: Gift cards, medication synchronization, discount programs
• Convenience: Evening and weekend appointments, telehealth options
• Education: Explain MTM value proposition clearly
• Multiple Touchpoints: Combine phone, SMS, email, and in-person invitations

Challenge 2: Time-Intensive Service Delivery

Problem: CMRs taking too long to be profitable

Solutions:

• Standardized Workflows: Templates and checklists for efficiency
• Pre-Visit Preparation: Review medication list before appointment
• Technology: Voice-to-text documentation, automated data population
• Focused Interventions: Prioritize high-impact issues
• Staff Support: Pharmacy technicians for data gathering
• Batch Scheduling: Group similar patients for workflow efficiency

Challenge 3: Limited Reimbursement

Problem: MTM revenue insufficient to cover costs

Solutions:

• Multiple Revenue Streams: Combine Part D, CPT codes, cash pay
• Increase Completion Rates: More CMRs = more revenue
• Upsell Services: Bundle MTM with adherence packaging, immunizations
• Efficiency Gains: Reduce per-service time through standardization
• Value-Based Contracts: Pursue ACO and quality-based payments
• Manufacturer Programs: Supplement with sponsored services

Challenge 4: Prescriber Engagement

Problem: Providers not responding to MTM recommendations

Solutions:

• EHR Integration: Send recommendations through provider workflow
• Concise Communication: Brief, actionable summaries
• Relationship Building: Personal outreach to key prescribers
• Data Sharing: Share outcomes demonstrating MTM value
• Collaborative Practice Agreements: Formalize pharmacist authority
• Face-to-Face Meetings: Present MTM program capabilities

Advanced MTM Services and Specialization

Diabetes Management Programs

Services:

• A1c point-of-care testing
• Continuous glucose monitoring (CGM) support
• Insulin titration protocols
• Medication optimization
• Lifestyle coaching

Technology Needs:

• Point-of-care testing devices
• Data management platforms
• CGM data integration
• Collaborative practice agreement templates

Hypertension Management

Services:

• Blood pressure monitoring programs
• Medication therapy optimization
• Home BP monitoring education
• DASH diet counseling

Technology:

• BP monitor validation
• Remote patient monitoring platforms
• Trending and reporting tools

Anticoagulation Management

Services:

• INR monitoring
• Warfarin dose adjustment
• Direct oral anticoagulant monitoring
• Bleeding risk assessment

Requirements:

• Point-of-care INR testing
• Dosing algorithms
• Collaborative practice agreements
• Quality assurance programs

Specialty Pharmacy MTM

Focus Areas:

• Oncology medication management
• HIV/AIDS therapy optimization
• Hepatitis C treatment support
• Rheumatoid arthritis biologic monitoring
• Multiple sclerosis disease management

Platform Requirements:

• Specialty medication databases
• Prior authorization management
• Financial assistance coordination
• Side effect management protocols
• Outcomes tracking for specialty drugs

Regulatory and Compliance Considerations

HIPAA Compliance for MTM

Privacy Requirements:

• Secure patient communication channels
• Encrypted data storage
• Access controls and audit logs
• Business associate agreements with software vendors
• Patient authorization for information sharing

State Scope of Practice

Verify Legal Authority For:

• Medication therapy management services
• Protocol-based prescribing
• Point-of-care testing
• Injectable medication administration
• Collaborative practice agreements

Documentation Requirements

Maintain Records For:

• 6-10 years (varies by state)
• All MTM encounters
• Patient communications
• Prescriber interactions
• Billing documentation

Quality Assurance

Implement Systems For:

• Peer review of clinical interventions
• Documentation audits
• Outcomes measurement
• Continuous quality improvement
• Patient safety event reporting

Future of MTM Software and Clinical Pharmacy

Artificial Intelligence Integration

Emerging Capabilities:

• Predictive analytics for patient risk stratification
• AI-powered medication therapy recommendations
• Natural language processing for documentation
• Automated identification of medication-related problems
• Chatbots for patient triage and education

Interoperability Expansion

Coming Improvements:

• FHIR-based EHR integration
• Real-time lab value access
• Bidirectional e-prescribing
• Social determinants of health data integration
• Prescription drug monitoring program (PDMP) connections

Value-Based Payment Models

Trends:

• Pay-for-performance MTM contracts
• Shared savings arrangements
• Population health management programs
• Bundled payment models
• Quality metric-based bonuses

Telepharmacy and Remote MTM

Expansion:

• Video-based CMRs as standard
• Remote patient monitoring integration
• Asynchronous MTM consultations
• Mobile app-based patient engagement
• AI-assisted virtual care

Getting Started with MTM Software

Step 1: Assess Your Readiness

Evaluate:

• Pharmacist interest and clinical skills
• Patient population MTM eligibility
• Technology infrastructure
• Time availability for MTM services
• Financial investment capacity

Step 2: Select MTM Software

Compare Platforms Based On:

• CMS compliance capabilities
• Integration with your pharmacy system
• Ease of use and training requirements
• Pricing model and total cost
• Payer network access
• Support and training offerings

Step 3: Enroll in Payer Networks

Complete:

• Medicare Part D MTM network applications
• NPI registration
• NCPDP provider credentialing
• Commercial payer contracting
• Credentialing verification

Step 4: Train Your Team

Provide Training On:

• MTM software navigation
• Clinical assessment skills
• Documentation standards
• Billing and coding
• Patient communication
• Workflow integration

Step 5: Launch and Monitor

Track Metrics:

• CMRs completed per week/month
• Completion rates by payer
• Revenue per service
• Medication-related problems identified
• Patient satisfaction
• Clinical outcomes

Conclusion: MTM Software as Foundation for Clinical Pharmacy

Medication Therapy Management software has evolved from simple documentation tools to comprehensive clinical pharmacy platforms enabling profitable, patient-centered services. In 2026, the most successful pharmacies view MTM not as a compliance burden but as a strategic opportunity to:

• Diversify Revenue: Beyond product dispensing
• Enhance Patient Outcomes: Measurable clinical improvements
• Differentiate Services: Compete on value, not just price
• Build Provider Relationships: Position pharmacists as essential care team members
• Future-Proof Practice: Align with value-based healthcare trends

Whether you choose OutcomesONE, Aprexis, DocStation, or PharmaPOS Clinical Module, the key is selecting a platform that integrates seamlessly with your workflow, provides robust clinical decision support, and enables efficient documentation and billing.

The MTM opportunity is substantial—Medicare beneficiaries alone represent millions of eligible patients, with commercial payers rapidly expanding programs. Pharmacies equipped with the right MTM software, trained staff, and systematic approach are building thriving clinical pharmacy practices generating six-figure annual MTM revenue.

Contact MedSoftwares today to learn how PharmaPOS Clinical Module can support your MTM services with integrated documentation, billing, and patient management tools designed for pharmacy workflow.

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