You can switch from athenahealth. Plenty of practices have done it. The honest caveat: it’s one of the harder EHRs to leave, for specific reasons that are worth naming before you start.
The percentage-of-collections pricing model means athenahealth earns a slice of everything you bring in. Third-party estimates put the rate at 4-7% of collections, though the actual figure depends on your contract and practice size (athenahealth doesn’t publish a rate card). If you want a full breakdown of what athenahealth costs before you calculate what you’d save, athenahealth EHR cost does that math in detail. Multi-year contracts with auto-renewal clauses are common. And if you’re on athenaCollector for RCM, you’re not just switching an EHR - you’re disentangling a billing engine too. None of that is insurmountable. It just means “I’ll switch next month” usually becomes a 60-90 day project when you plan it properly.
The destination in this guide is Patient Square’s AI Copilot EHR, which ships inside the Copilot tier at $119 per clinician per month on annual billing. Flat. Per clinician. No percentage of anything. Book a demo and you can see a finished note in two minutes before you touch your contract.
Key takeaways
- athenahealth’s percentage-of-collections model (commonly 4-7%, per third-party estimates) scales against your revenue. A flat $119/mo per clinician is a different economic structure entirely.
- Contracts typically auto-renew; check your MSA for the notice window before you plan a go-live date.
- athenahealth does provide data export (EHI, CCDA, clinical chart) via athenaOne - request it early.
- If athenaCollector is your RCM engine, the billing transition is a separate workstream from the EHR switch. Plan for both.
- Patient Square is an AI EHR and scribe - not a full RCM replacement. That’s the honest trade-off.
- A 7-day parallel trial lets you validate note quality on real visits before you commit.
The honest difficulty map
Before the step-by-step, a table. The friction is real in some places and manageable in others.
| What you’re moving | The friction | How to handle it |
|---|---|---|
| Patient records & clinical data | EHI/CCDA export exists but needs advance planning; post-shutdown exports take weeks | Request export 30+ days before termination; download and verify before closing account |
| Contract / notice period | Multi-year contracts with auto-renewal are common; early termination fees can be substantial | Read your MSA now; time your switch to a renewal window if possible |
| RCM / billing (athenaCollector) | Leaving means replacing your billing workflow too | Decide: standalone biller, clearinghouse, or new RCM vendor - plan this in parallel |
| New note documentation | Ramp period on any new system | 7-day parallel trial removes the guesswork before you cut over |
| Note portability going forward | Patient Square notes export as PDF, HL7, FHIR | You’re never locked in again - EHR-ready export any time |
How the two pricing models compare
| athenahealth | Patient Square (Copilot tier) | |
|---|---|---|
| Model | Percentage of collections | Flat per clinician |
| Rate | ~4–7% of collections (third-party estimates; rate varies by contract) | $149/mo month-to-month, $119/mo annual |
| 500-visit/month practice at $300K annual collections | ~$12,000–$21,000/year (at 4–7%) | $1,428/year per clinician on annual billing |
| Predictability | Scales with revenue; rises when collections rise | Fixed - same bill every month |
athenahealth rate is a third-party estimate; the actual rate is set in your contract. Verify your own MSA.
Why athenahealth is genuinely hard to leave
Three things create the stickiness, and knowing them upfront makes the switch less surprising.
The RCM entanglement. athenaCollector is a real billing engine: claims scrubbing, denial management, patient billing follow-up. It’s one of the reasons practices choose athenahealth in the first place. When you leave, that workflow needs a home. You’re not just picking a new place to write notes. You’re re-solving a billing problem.
The contract structure. athenahealth contracts commonly run multiple years with auto-renewal clauses and termination fees. This isn’t unusual for enterprise software, but it does mean the decision to switch needs to be made with your renewal date in mind, not spontaneously. Pull out your MSA and find the notice clause before you call anyone.
The data export friction. The export tools exist: EHI export, CCDA export, and clinical chart export are all available inside athenaOne. What bites practices is not requesting the export early enough, or not verifying the files before closing the account. Post-shutdown exports exist as a fallback but take weeks and may involve additional fees.
None of these are reasons to stay if the fit isn’t right. They’re reasons to plan.
The 6-step migration plan
Step 1: Pull your contract and find your notice window
Before you tell anyone you’re leaving, find your MSA. Look for the termination notice requirement (often 60–90 days), auto-renewal language, and any early-termination fee clauses. If your renewal window is coming up in the next few months, that’s your cleanest exit. If you’re mid-contract, factor in the fees when you calculate the cost of switching.
Step 2: Request your data export from athenahealth
Log into athenaOne, go to Manage Data Exports, and request your EHI export, CCDA export, and clinical chart export. Also export patient demographics and billing data. Do this 30 or more days before your intended termination date. Download and verify the files. athenahealth retains your exported data for one calendar year from file creation if you chose Practice Files, but you don’t want to depend on that.
Step 3: Decide your RCM path
This is the fork in the road. If you’re using athenaCollector as your billing engine, you need a plan for what replaces it: a standalone billing service, a clearinghouse relationship, or a new RCM vendor. This timeline runs in parallel with your EHR transition, not sequentially. Sorting out the billing path before you pick your go-live date prevents the most common migration delay.
Step 4: Run Patient Square in parallel during the 7-day trial
Start your 7-day free trial and run it on real visits alongside athenahealth. Don’t rely on a demo. Use your actual patient types, your specialties, your note templates. The AI Medical Scribe is one module inside Practice Copilot, Patient Square’s AI platform for the whole practice, and it listens during the visit and hands back a structured SOAP note, ICD-10 suggestions, and a prescription draft, ready to review and sign about two minutes after the visit. By day 3 or 4 you’ll know whether the note quality holds up for your workflow.
The Copilot tier (which includes the bundled AI Copilot EHR) is $119 per clinician per month on annual billing. That’s the tier you’re evaluating for the full EHR switch.
Step 5: Move documentation
Once you’re satisfied with note quality, shift your active documentation to Patient Square. Your historical records stay accessible in your exported athenahealth files; you’re not erasing the clinical history, you’re just writing new notes in a new system. Your clinical staff typically adapts faster than the billing side.
Step 6: Cut over and close your athenahealth account
Give the termination notice per your contract: in writing, to the right contact, with the right lead time. Confirm receipt. Verify your exported files one more time before the account closes. If you need anything post-shutdown, request it promptly - the timeline for post-shutdown data requests runs weeks, not days.
When you should stay on athenahealth
This belongs in a switching guide. Not every practice should leave.
If athenaCollector is central to your revenue cycle and you don’t want to unbundle it (the denial management, the claims scrubbing, the patient billing follow-up as an integrated system), then switching EHRs without solving the RCM side is a bad trade. Patient Square is not a full RCM replacement. The bundled AI Copilot EHR handles documentation, scheduling, eRx drafts, and ICD-10 suggestions. It is not athenaCollector.
Stay if: the billing integration is the thing you’re buying athenahealth for, and you’re not ready to build a new billing workflow.
Switch if: the documentation burden is the pain, the percentage-of-collections bill is rising faster than your satisfaction with the tool, and you’re willing to handle billing separately.
Note portability you won’t have to fight for
One of the quieter costs of EHR entrenchment is the exit friction. You just spent this guide planning a way out of a system that made leaving complicated. Patient Square’s notes export as EHR-ready export (PDF, HL7, FHIR) - that’s the exact phrase we use because it’s the accurate one. Export or delete any visit, any time. Audio is processed in memory and discarded the moment the note drafts. No recording retained. Your notes belong to your practice, and when the next renewal conversation comes around, you’re not trapped.
For more on why data ownership is the right criterion when evaluating AI scribes, see our data ownership and export guide.
For practices already mid-search across several tools, the AI scribe vs new EHR comparison covers the decision frame in depth.
How to run the parallel trial in a week
Concrete steps for the 7-day window:
- Sign up for the trial - no card, no call required.
- Pick 10–15 visits across your most common appointment types.
- Run Patient Square on each one alongside your current charting process.
- Review the draft SOAP note, ICD-10 suggestions, and prescription draft for each.
- By day 4–5, score the notes against your usual standard: does this save 30–45 minutes of end-of-day charting, or not?
- If yes, request a demo call to map the Copilot EHR to your practice setup before you give athenahealth notice.
The migration checklist for switching your AI scribe walks through the documentation-workflow side in more detail if you want a parallel reference.
One more thing worth checking if you’re evaluating the broader EHR market alongside this: best EHR for small practices covers what to look for beyond the vendor’s own pitch.
Patient Square’s pricing page has the full tier breakdown with no asterisks. Security details (encryption, access controls, BAA availability, SOC 2 Type II audit status) are on the security page. The 7-day trial is on the same pricing page. Book a short demo first if you want to see the note against your own visit type; run the trial in the same week.