7 EHR selection pitfalls that could cost your practice

Why the right EHR choice matters for physicians

Choosing the wrong Electronic Health Record (EHR) can disrupt clinical workflows, frustrate providers, and create long-term financial and operational challenges. Unlike typical software, EHRs become deeply embedded in every aspect of your practice, and the consequences of a poor choice can compound over time. Knowing the warning signs before you sign a contract is the best way to protect your practice from hidden risks of EHR problems.

This guide highlights common pitfalls to watch for during vendor evaluation, so you can avoid costly mistakes and select a system that supports your practice today and in the future.

Seven EHR selection pitfalls every practice should know

Industry research shows that about 30% of practices replace their EHR within three years, and transitions often bring steep costs — costing practices hundreds of thousands of dollars in the first year alone, along with measurable productivity losses.

These high stakes make knowing what to avoid in an EHR vendor as important as what to look for. Here a seven weakness to look for:

Knowing the warning signs before you sign a contract is the best way to protect your practice from hidden risks of EHR problems.

#1: Lack of true interoperability

Some vendors advertise interoperability but quietly lock your data into proprietary formats, making transitions difficult and stalling collaboration across labs, hospitals, and external care networks. Without genuine data exchange, your staff spends more time chasing records, while care coordination and reporting suffer. This not only slows clinical decision-making but also puts your practice at risk of failing quality programs that depend on accurate, timely data.

Red flags to watch for:

• Limited integration with your existing tools or partners, forcing manual workarounds
• No support for FHIR or HL7 standards, which are essential for seamless data exchange
• Closed or poorly documented APIs that make integrations costly or impossible

Choosing an EHR without true interoperability risks isolating your practice from your broader care network and adding inefficiencies that only grow over time.

Ask vendors: How do you support FHIR- and HL7-based integrations with external labs, hospitals, and referral partners?

#2: Hidden fees and lock-in contracts

An EHR that looks affordable upfront can become one of your biggest long-term expenses if the vendor relies on hidden costs and restrictive terms. Practices often discover too late that switching vendors is financially prohibitive, or that scaling their system to match growth comes with a steep price tag. These costs don’t just strain budgets — they can delay technology upgrades, limit hiring, and weaken financial stability.

Red flags to watch for:

• Prohibitive data export fees that make it costly to leave or transition to a new system
• Long-term contracts with harsh early termination penalties that trap you in a poor fit
• EHR pricing models that escalate sharply as your practice grows, eroding any initial savings

These tactics can leave your practice overpaying while stuck with a system that no longer serves your needs. Transparent discussions about EHR pricing and total EHR cost help you avoid being surprised later.

Ask vendors: What are the total costs for data migration, user scaling, and early contract termination?

#3: Poor patient engagement features

Patients now expect the same digital convenience from their healthcare providers that they experience in other areas of life. An EHR without modern patient-facing tools can weaken communication, reduce adherence to care plans, and hurt overall satisfaction. These gaps don’t just affect patient experience — they can also drag down quality scores and value-based care performance, where engagement is tied directly to reimbursement.

Red flags to watch for:

• Outdated or limited patient portals that make accessing records or messaging providers difficult
• No mobile app or SMS/email capabilities, leaving patients without convenient ways to engage
• Lack of telehealth support, which limits care access and flexibility

Without robust engagement tools, your practice risks frustrating patients and missing opportunities to improve outcomes and secure incentives under value-based programs.

Ask vendors: Can patients access and update their health information through mobile and web? Do you support SMS/email reminders, telehealth, and remote monitoring within the EHR?

#4: Ineffective support and training

Even the most advanced EHR can fail if your team can’t use it effectively. A steep learning curve or lack of vendor support often results in prolonged disruptions, lower productivity, and mounting frustration among staff and providers. Training and support are also critical for long-term ROI — without them, new features often go unused and workflow improvements stall.

Red flags to watch for:

• Minimal or generic EHR training programs that don’t address your practice’s specific workflows
• Slow or inconsistent response times for troubleshooting issues
• Little to no ongoing education or resources to help staff adopt new features over time

Without EHR training and reliable support for physicians and staff, your investment in a new EHR may never deliver its full value — and your team may never feel confident using it.

Ask vendors: What training options do you provide before, during, and after implementation? How quickly does your support team respond to urgent issues, and what resources are available for ongoing education?

#5: Overly rigid systems

Healthcare is constantly evolving, and your EHR needs to evolve with it. A system that can’t adapt to new care models, reimbursement structures, or regulatory requirements quickly shifts from being a tool to being a hindrance. Flexibility isn’t optional — it’s essential for keeping pace with the industry. Rigid systems also increase compliance risks, since regulatory delays or workarounds could potentially expose your practice to penalties and lost revenue.

Red flags to watch for:

• No configurable workflows or templates, forcing your practice into one-size-fits-all processes
• Slow or costly updates when regulations change, leaving you vulnerable to compliance issues
• Limited ability to integrate emerging tools, such as AI-driven healthcare analytics and automation

An inflexible EHR locks your practice into outdated processes and technologies and creates long-term risks that go beyond inconvenience.

Ask vendors: How often do you release system updates, and how quickly do you adapt to regulatory changes? Can workflows and templates be customized to match our practice’s needs without costly development?

#6 Incompatibility with specialty needs

General-purpose EHRs often overlook the unique workflows and documentation requirements of specialties such as behavioral health, women’s health, or orthopedics. Without built-in support, practices are forced into costly customizations or inefficient workarounds that frustrate providers and slow down care delivery. Specialty gaps also impact productivity, as providers spend more time documenting manually instead of focusing on patients.

Red flags to watch for:

• Missing specialty-specific fields or workflows, requiring heavy manual input
• Dependence on third-party add-ons to meet core clinical needs
• Little experience supporting your specialty, leaving you without proven best practices

An EHR that isn’t built with your specialty in mind can drain resources and compromise the quality of care — while putting your providers at greater risk of burnout. A specialty EHR designed for your field provides templates, workflows, and best practices out of the box.

Ask vendors: What specialties do you serve today, and can you provide client examples in our specialty? Do you offer pre-built templates and workflows specific to our field.

#7: Short-term cost focus over long-term value

An EHR that looks inexpensive at the outset can end up costing far more in the long run. Hidden maintenance fees, downtime, and inefficiencies quickly erode any savings, while a lack of scalability limits your ability to grow. Evaluating only the upfront price overlooks the system’s true total cost of ownership. This short-term mindset also makes practices more vulnerable to vendor churn, since they may be forced to replace the system sooner than expected.

Red flags to watch for:

• Frequent downtime or performance issues that disrupt care and revenue flow
• High maintenance or upgrade costs that inflate the budget over time
• No scalability or future-focused support, forcing another replacement down the road

Focusing only on initial savings can leave your practice paying more while competitors move ahead with systems that improve efficiency and support long-term growth. Carefully assessing EHR pricing models and projecting the full EHR cost over time helps avoid surprises.

Ask vendors: What is your track record on uptime, and how do you measure performance? How do costs scale as we add providers or locations? Can you demonstrate the long-term ROI practices have achieved with your system?

EHR for physicians: How to choose with confidence

Selecting an EHR is one of the most strategic decisions your practice will make. By recognizing these seven pitfalls, you can spot red flags early, ask the right vendor questions, and evaluate systems with confidence. This preparation helps you avoid costly mistakes that disrupt care, frustrate providers, or stall growth.

Ready to evaluate with confidence? See how athenaOne® helps practices sidestep these pitfalls and deliver measurable value from day one.