What a primary care practice needs from its software
Family medicine, internal medicine and pediatrics share one trait: a high volume of short visits across a wide range of problems, with many patients seen for years. That shapes the software more than any single feature list.
A certified EHR, because Medicare programs depend on it. If your clinicians take part in MIPS, the Promoting Interoperability category is built on certified EHR technology. Check that the product and version you are buying are on the ONC Certified Health IT Product List (CHPL). Elation EMR, Practice Fusion and AdvancedMD state that they are ONC-certified in their reviews, and eClinicalWorks publishes its certification disclosures. Medicare's chronic care management rules also require that patient demographics, problems, medications and allergies be recorded in a certified EHR.
Immunization registry reporting. For the 2026 MIPS performance period, Immunization Registry Reporting is a measure in the Public Health and Clinical Data Exchange objective. The clinician attests to active engagement with a public health agency to submit immunization data and receive forecasts and histories from the state immunization information system. If the practice registers for the first time, registration must be done within 60 days of the start of the performance period. Pediatric and family practices give the most vaccines, so a working, two-way registry interface matters more here than in most specialties. eClinicalWorks lists registry reporting in every plan, and CharmHealth and AdvancedMD list immunization registry reporting in their EHRs.
e-Prescribing with EPCS. Primary care writes many controlled substance prescriptions, from ADHD medication to pain and sleep drugs. CMS requires that at least 70% of a prescriber's Medicare Part D Schedule II to V prescriptions be sent electronically, unless the prescriber qualifies for an exception, such as writing 100 or fewer qualifying Part D controlled substance prescriptions a year. The software must meet all DEA requirements. In practice that means identity proofing for each prescriber and two-factor signing. Practice Fusion includes EPCS in its provider license. Others charge for it: Office Ally lists EPCS at $100 per provider per year plus the token cost, and AdvancedMD lists EPCS at typically $35 a month.
Lab interfaces. Primary care orders labs at a high rate, usually through Quest, Labcorp or a hospital lab, and needs results back in the chart. Ask whether the interface already exists and who pays to build it. CollaborateMD, for example, lists Quest and Labcorp interfaces at $2,500 each and notes that the labs normally pay that fee. If you run waived tests in the office, such as rapid strep or urine dipsticks, you also need a CLIA certificate, and the EHR should let staff enter point-of-care results.
Care management and wellness billing. Chronic care management (CPT 99490 and related codes) needs patient consent, a comprehensive electronic care plan and 24/7 access to care, and the clinical staff time has to be tracked each month. CMS's June 2025 booklet adds advanced primary care management codes (G0556 to G0558), which are tiered by the number of chronic conditions. You can bill remote physiologic monitoring or remote therapeutic monitoring alongside CCM, but not both. The Medicare annual wellness visit, covered once every 12 months, needs a health risk assessment, a cognitive assessment and a written screening checklist. Your EHR should have templates for these visits, time tracking for care management and reports that show which patients are due.
A patient portal patients will use. Primary care runs on refill requests, lab results and short questions. A portal and secure messaging take some of that load off the phones. eClinicalWorks and Elation both include a portal in their EHR plans.
A front desk that can handle the phones. Primary care phone lines are busy with same-day sick visits, refill calls, referral questions and results calls. When calls go unanswered, patients book elsewhere. This is where AI phone agents, answering services and shared-inbox phone systems earn their cost.
All-in-one or separate tools?
For most practices in this size range, one EHR should cover charting, e-prescribing with EPCS, labs, registry reporting, the portal and MIPS.
The real choice is how to bill. There are three common patterns:
- EHR and billing from one vendor. eClinicalWorks sells EHR plus practice management, and also offers RCM as a percentage of collections. athenahealth sells athenaOne as EHR, practice management and billing in one, priced as a share of collections, with athenahealth RCM as the billing layer. Tebra bundles EHR, billing and patient marketing.
- A clinical-first EHR plus a billing tool. Elation Health is built for primary care and offers its own EHR and billing bundles, or you can keep a separate billing system such as CollaborateMD, which works with outside EHRs.
- Low-cost EHR plus outsourced billing. Practice Fusion or CharmHealth for charting, with a billing service such as Athelas. Office Ally is a common low-cost choice for claims and practice management.
After billing, the tools that most often sit outside the EHR are:
- An ambient AI scribe. Primary care visits cover several problems in a short slot, and notes pile up at the end of the day. Freed and Heidi Health work alongside any EHR. Sunoh is the natural fit on eClinicalWorks. Suki is sold mainly to larger medical groups. Elation and AdvancedMD sell their own AI add-ons, so compare those first.
- Phones and front desk. Assort Health books appointments straight into athenahealth and other EHRs by voice AI. Lydoh answers calls and passes structured requests to staff. Ambs Call Center and PatientCalls offer live answering for overflow and after hours. Spruce Health combines phone, text, fax and video in one shared inbox.
- Reminders and recall. If your EHR's reminders are basic, Weave, Solutionreach or Relatient can run reminders, recall for wellness visits and two-way texting.
- Compliance. A program such as Accountable or Compliancy Group for policies, training and the security risk assessment, plus Paubox if staff email patient information.
A separate e-prescribing tool such as RXNT only makes sense if your EHR lacks EPCS. The same goes for telehealth: most primary care EHRs include video or sell it as a small add-on, and Doxy.me has a free plan for occasional use.
What primary care software costs
As of November 2026, these are the published prices behind the ranges below:
- EHR: Practice Fusion from $199 per provider per month with an annual commitment. CharmHealth's Provider Plan at $200 per provider per month. Elation Standard EHR at $425 per provider per month, or $699 with billing. eClinicalWorks at $499 per provider per month for the EHR only, or $599 with practice management, with no start-up costs. AdvancedMD lists $429 to $1,070 per provider per month for medical specialties. athenahealth does not publish prices.
- Billing services: eClinicalWorks RCM at 2.9% of collections. AdvancedMD RCM at 4% to 8% of collections. CollaborateMD billing software typically from $299 per provider per month, with no setup fees.
- AI scribe: Freed Core at $59 to $79 per clinician per month, depending on billing term. Sunoh at $149 per user per month, a limited-time price. Elation Note Assist at $199 per provider per month. AdvancedMD's AI add-on at $100 per provider per month.
- Front desk: Lydoh from $99 a month for after-hours answering, or $249 for the Frontdesk plan with 1,200 voice minutes, then $0.25 a minute. Spruce at $24 or $49 per user per month. Ambs Call Center live answering from $149 a month for 100 minutes, plus an $85 setup fee.
- Engagement and compliance: Weave plans start at $199 a month. Accountable Basic HIPAA at $169 a month billed annually. Paubox Email Suite Standard at $32 a month billed annually for up to 5 senders, or $85 for 10.
Rough software totals, not counting staff salaries:
| Practice | Lean stack | Typical stack |
|---|---|---|
| Solo | about $400 a month ($4,800 a year) | about $2,200 a month ($26,400 a year) |
| 3 providers | about $950 a month ($11,400 a year) | about $5,300 a month ($64,000 a year) |
| 10 providers | about $2,500 a month ($30,000 a year) | about $17,400 a month ($209,000 a year) |
The lean stack is Practice Fusion, Accountable and Paubox, with billing done in-house. The 3-provider lean stack adds Lydoh's After Hours plan. The typical stack is eClinicalWorks EHR with practice management, eClinicalWorks RCM at 2.9% (assuming $30,000 in monthly collections per provider), Freed Core, Lydoh or Spruce for the phones, Weave, Accountable and Paubox. Percentage billing is the biggest line once collections grow, so get two quotes before you sign. eClinicalWorks includes initial training only for practices with 1 to 9 providers, and larger practices pay implementation fees.
To model your own numbers, use the software cost calculator.
Compliance checklist for primary care practices
- HIPAA security risk assessment. The HIPAA Security Rule requires covered entities and business associates to do a risk assessment. ONC publishes a free Security Risk Assessment Tool for small practices.
- Business associate agreements with every vendor that stores or handles patient information: EHR, billing service, scribe, phone system, answering service, texting tool and email encryption.
- Certified EHR for MIPS. Confirm the product and version on the CHPL before the performance period starts, and keep your CMS EHR Certification ID.
- Immunization registry engagement. Register with your state immunization information system within 60 days of the start of the performance period if you have not registered before, and respond to its requests within 30 days. Missing two requests in a performance period means you do not meet the measure.
- EPCS. Use DEA-compliant e-prescribing software, finish identity proofing and two-factor setup for each prescriber, and check your Part D compliance status in the CMS EPCS Prescriber Portal. Keep your email and mailing address current in PECOS and NPPES, because CMS uses them for notices.
- Chronic care management. Get and document written or verbal consent before billing CCM, keep an electronic care plan, and offer 24/7 access to care. Do not bill RPM and RTM together alongside CCM.
- Annual wellness visits. Use a template that captures the health risk assessment, cognitive assessment and written screening schedule, and check that the patient is past 12 months since their last wellness visit and their Part B enrollment.
- CLIA certification for any lab testing done in the office, including waived tests.
- OSHA Bloodborne Pathogens Standard (29 CFR 1910.1030). Keep a written exposure control plan covering engineering controls, protective equipment, training and hepatitis B vaccination for staff who draw blood or give injections.
Questions to ask in a demo
- Which version of your EHR is on the CHPL, and what is our CMS EHR Certification ID?
- Do you have a live, two-way interface with our state immunization registry, and who handles registration and testing?
- Which MIPS measures does your dashboard track, and can you submit Promoting Interoperability and quality data for us?
- Is EPCS included? What do identity proofing and tokens cost per prescriber, and is PDMP checking built in?
- Do you already have live interfaces with Quest, Labcorp and our hospital lab? Who pays the interface fee?
- How do you track chronic care management time, consent and care plans? Can you report which patients qualify?
- Do you have annual wellness visit templates with the health risk assessment and cognitive assessment, and a recall list of patients who are due?
- Do you support remote patient monitoring device data, and how is that time tracked?
- What can patients do in the portal: refills, messages, lab results, scheduling, forms, payments?
- Can your phone or AI tools book appointments directly into our schedule, or do staff still have to enter them?
- What does the AI scribe cost per clinician, and does it push notes and codes into our EHR?
- What are the contract length, setup fees and data export terms if we leave?