Selecting the Best EHR System for Small Nonprofits
Looking for the best EHR systems for your nonprofit? Managing community health data can be overwhelming without the right tools. Electronic Health Records (EHR) systems streamline documentation, enable secure data access, and support collaborative care—making them essential for modern nonprofits delivering health and human services.
But with limited budgets, evolving grant requirements, and small teams, choosing the right EHR for a nonprofit can feel like navigating a maze.
In this blog, we compare the top EHR systems designed for small nonprofits and community-based organizations and share a step-by-step guide to help you pick the right fit. Whether you're just starting or looking to switch, this guide will help you make an informed choice.
Why Nonprofits Need EHR Systems
Nonprofits dealing with healthcare, case management, or wraparound services often juggle multiple responsibilities—service delivery, compliance, referrals, and reporting.
An EHR tailored for nonprofits helps by :
- Centralizing client records securely and efficiently
- Supporting referral workflows between providers and community partners
- Improving data reporting for grants and compliance (HIPAA, SAMHSA, etc.)
- Reducing paperwork and enabling real-time updates from staff and volunteers
- Ensuring continuity of care across programs
Key Features to Look for in a Nonprofit-Focused EHR System
Before diving into the systems, let’s outline what small nonprofits should prioritize in an EHR platform :
| Feature | Why It Matters |
|---|---|
| Ease of Use | Staff and volunteers need minimal training |
| Referral Tracking | Seamless coordination with external partners |
| Compliance Support | Built-in HIPAA & grant reporting tools |
| Custom Workflows | Flexibility to match your service delivery model |
| Affordable Pricing | Transparent, nonprofit-friendly pricing |
| Offline Access / Mobile Use | For outreach and fieldwork teams |
Top EHR Systems for Small Nonprofits
Here’s a curated list of EHR solutions with a strong focus on small to mid-sized nonprofits. We’ve highlighted their unique advantages and considerations.
1. Pillar by SocialRoots.ai – Built for Nonprofits from the Ground Up
Why Choose Pillar?
Pillar is purpose-built for nonprofits and community organizations. It goes beyond basic EHR functions—offering integrated tools for care planning, referrals, volunteer coordination, and grant reporting.
Key Benefits :
- User-friendly interface with minimal training required
- HIPAA-ready, with encrypted data handling
- Built-in referral management and collaboration across organizations
- Customizable care plans and social determinants tracking
- Transparent pricing designed for nonprofits
Explore Features | Explore Features
Best For : Community health nonprofits, Hospital and Clinics, CBOs, housing support, and multi-service organizations.
2. Foothold Technology (AWARDS) – For Behavioral Health and Human Services
Why Choose AWARDS?
Foothold's EHR system is highly configurable and caters to behavioral health and substance use nonprofits.
Key Benefits :
- Deep specialization in mental health and human services
- Custom forms, assessments, and program tracking
- Strong compliance features (including OMH, HUD, etc.)
Considerations :
Slightly steeper learning curve; pricing may vary with customization.
3. NextGen Office – Clinical EHR for Federally Qualified Health Centers (FQHCs)
Why Choose NextGen?
This is a full-featured clinical EHR designed for small medical clinics and FQHCs.
Key Benefits :
- Built-in e-prescribing, billing, and clinical workflows
- UDS and Medicaid/Medi-Cal reporting support
Considerations :
Heavily medical-focused; may be too complex for non-clinical nonprofits.
4. AthenaOne (Athenahealth) – For Growing Clinical Teams
Why Choose AthenaOne?
Offers a complete suite of EHR, billing, and patient engagement tools.
Key Benefits :
- Cloud-based with robust scheduling and billing
- Scalable with AI features for clinical insights
Considerations :
More expensive than nonprofit-first tools; optimized for medical practices.
5. CareLogic by Qualifacts – Tailored for Behavioral and Mental Health Providers
Why Choose CareLogic?
Popular among small behavioral health nonprofits and counseling services.
Key Benefits :
- Detailed treatment plan templates
- Integrated telehealth and outcome tracking
- Flexible compliance reporting
Considerations :
Longer implementation time; requires some technical setup.
How to Choose the Right EHR system for Your Nonprofit: A Step-by-Step Guide
Choosing the right EHR is less about the number of features and more about fit. Here’s how to make the right call :
Step 1: Assess Your Needs
- Are you primarily focused on medical care, case management, or wraparound services?
- Do you need referral tracking or care coordination features?
- What are your grant or compliance obligations?
Step 2: Involve Your Team
Include program leads, IT staff (if any), and frontline users in demos and decision-making. Ease of use often makes or breaks adoption.
Step 3: Consider Long-Term Scalability
- Will the EHR grow with you as you add new programs or partners?
- Does it offer integration with third-party tools (like Salesforce, HMIS, etc.)?
Step 4: Evaluate Pricing Transparency
Many EHR vendors don’t list pricing upfront. Look for nonprofit-friendly pricing models—like those offered by Pillar, which includes transparent tiers with no surprise fees.
Step 5: Request a Demo & Trial
Before committing, request a live demo or a trial period to test workflows with your team.
Why Pillar is a Top Choice for Small Nonprofits
Pillar by SocialRoots.ai was developed specifically for nonprofits working in complex community care ecosystems. Whether you're managing case notes, coordinating referrals, or preparing reports for funders, Pillar provides a clean, easy-to-use platform that meets your mission needs without the enterprise cost.
You’ll benefit from :
- Rapid onboarding for small teams
- Tools for volunteers and community stakeholders
- Compliance-ready reporting
- Scalable structure without steep licensing models
Ready to see how Pillar works in action?
Final Thoughts
Selecting the right EHR is one of the most important technology decisions your nonprofit can make. The best system isn't necessarily the most complex—it’s the one that empowers your staff, simplifies compliance, and supports better outcomes for your community.
Pillar stands out as a nonprofit-first EHR platform that simplifies documentation, strengthens care coordination, and helps your team stay focused on what matters most: serving people.