When choosing an EHR software, you'll need to look out for a few hidden costs as well. To estimate an accurate ROI, you'll need to factorize the direct EHR costs of implementation such as licensing and hardware and indirect (or hidden) costs as well. Hidden cost of EMR software usually include employee training, customized changes in the EHR, assistance in implementation, and more. In this article, we'll be going over some of the high hidden costs of implementing an EMR software you may face.

The top hidden costs of implementing an EMR software include:

  • Patient Portals
  • Customized Changes
  • Add-Ons & Upgrades
  • Temporary Productivity Loss
  • Migrating Data and Conversions
  • Implementation Assistance
  • Employee Training
  • Maintenance
  • Security Features

These hidden costs may differ based on the EHR you're implementing. There are a few EHR service providers that minimize hidden costs for physicians.

Patient Portal

A patient portal is one of the most helpful EHR software features that enables you to connect with patients seamlessly. However, a patient portal's setup costs can go up to $450 with a monthly fee of up to $100. Some EHR service providers have started offering a patient portal as a part of an EHR software and removing the need for additional charges. These include CureMD EMR, AdvancedMD EHR, Athenahealth EMR, to name a few.

Customized Changes

When you install a new EHR system, you might need to tweak and adjust the solution to fit your environment. Practices often require more than the essential services of an EHR. So you would need to customize your EHR software inevitably. However, you can reduce the cost of personalized changes by selecting an EHR service provider that offers extensive user configurations.

Add-Ons & Upgrades

To benefit from the best services that your EHR vendor has to offer, you would need to upgrade your EHR now and then. However, upgrading your EHR software is a costly endeavor. With the new changes in E/M coding coming from Jan 1st, 2021, you might need to upgrade to the latest EHR version. To better facilitate the changes, you might also need to implement add-on services. With add-on services, you might need to pay an additional amount every month.

Temporary Productivity Loss

You might be wondering, why would you experience a temporary productivity loss if an EHR software is supposed to improve productivity? When you implement EHR software, it takes a certain amount of time for your staff to get used to the new system and use all the features required efficiently. So there's a small learning curve that you'll have to experience after implementing an EHR software that temporarily reduces productivity.

Some EHR software help minimize this effect by providing an easy-to-use interface and training manuals/tutorials.

Migrating Data and Conversions

EHR software help practitioners view patient information, check lab results, review prescriptions, etc., with ease. However, when you implement EHR software, migrating your patient information from your previous system to the new system can be costly. Multiple factors come into play here that affect how easily you can migrate your data. These include the capabilities of your database, the option to import data within your EHR, etc.

According to an estimate, data migration costs can go as high as $30,000 to $40,000, depending upon the practice's size, complexity, and nature.

Implementation Assistance

While most EMR companies cover implementation costs in their setup fees, you will have to pay extra if you are looking for onsite implementation or training assistance. It can be an expensive endeavor as apart from paying for their services, you are often asked to cover their transportation cost, which can be significant.

For more details, check out our guide on implementing EHR for small practices.

Employee Training

Your staff will need training for the new EHR system. It includes your nursing staff, physicians, office, and administration staff. Although most EMR companies offer 20 hrs of training for free, any additional training hours will come at a cost. Most EHR service providers follow the standard rate of $1,000 per day for further training. You can avoid this cost by using online prerecorded training modules provided by your vendor or having a master trainer trained in your practice who can teach others.


In addition to the implementation and purchasing costs, you might also need to pay a certain amount of maintenance fee annually. However, there are recent trends that indicate a decreasing rate of maintenance cost. Most EHR service providers choose not to charge any annual maintenance fees to improve their client relations.

Security Features

Compliance with HIPAA and HITECH guidelines reduces the chances of a data breach, but they don't wholly ensure data safety. To maximize your security, you'll need to implement security protocols and features.

Final Words – Steer Clear from Hidden Costs

Whether you implement an EMR for regulatory purposes or to increase your practice's operational efficiency, there are costs both upfront and hidden that you must be aware of before choosing a vendor. It is ideal to have a conversation about these costs with your prospective EMR software companies from the get-go to avoid any unpleasant surprises in the future. You will enter into long-term contracts with these companies, so it's always better to be safe than sorry.