What your first 90 days on a new EHR look like

Key takeaways

Go-live isn’t the finish line. It’s the start of a 90-day window where your clinical data is still converting, your billing team is running two systems, and the person at your EHR vendor who guided your implementation is about to hand you off to someone new. On top of that, the IT, security, and reporting questions that nobody raised during the sales process are going to start surfacing. Here’s what to expect and when.

Go-live day feels like the end of a long process. You’ve been through demos, contract negotiations, implementation, training, and now the switch is done. Your team is in the new system.

But for the next 90 days, there’s a lot happening underneath that most practices don’t see coming. And the reason it catches people off guard is that nobody walks them through what the EHR post-go-live period looks like before they get there.

This is what we cover with practices, so they know what to expect.

What’s happening during those 90 days

There are at least four things running simultaneously in your EHR post-go-live window, and most practices don’t realize they overlap until they’re in the middle of it.

The first thing to understand is that these aren’t sequential. They’re all running at the same time. Your team is documenting in the new system, looking up historical notes in the old system, billing out of both systems, waiting for the clinical data to convert, and somewhere in the middle of all of that, the person at the EHR vendor who’s been guiding your implementation hands you off to someone new.

That overlap is what makes the first 90 days feel chaotic, even when everything is going according to plan.

The clinical conversion is running in the background

The clinical conversion, your chart documents, visit notes, and full patient record doesn’t move until after go-live. Your providers document in the current system right up until switch day, then the old vendor extracts a complete snapshot once everything is signed off and closed out. We convert from that.

From the time we receive the data, the clinical conversion usually takes six to eight weeks. During that window, your team keeps two tabs open: everything new goes into the new EHR, and if someone needs to reference a historical chart note, they click back into the old system.

The two-tab period is temporary, but it’s real, and it helps to tell your providers what to expect before go-live day rather than on it. The most common frustration we hear isn’t that the process takes too long. Nobody told the clinical staff it was going to work this way.

Your billing is in two places

At the same time, the clinical conversion is running, your billing team is managing a wind-down in your old system.

Everything that was already in the claims pipeline before go-live stays in the old system. You work it down over time. New visits bill out of the new EHR. That billing wind-down typically runs 90 to 120 days, and during that stretch, your billing team is effectively working in both systems.

This is the part that tends to create the most operational stress, because:

• Your billing team may not have been part of the implementation conversations and might not know this is coming
• The clearinghouse connections in your old system need to stay active until those claims are fully worked
• Reporting is split across two platforms during the wind-down, which makes it harder to get a clean picture of your revenue cycle. If your CFO or practice administrator needs a monthly collections report, they’re pulling data from both systems and reconciling manually until the wind-down is complete. If leadership is used to a single dashboard view of revenue cycle performance, that view doesn’t exist for the first 90 days unless someone builds it.
• The person who manages your billing needs to be in the loop early, not on go-live day

If there’s one thing we’d recommend doing before you go live, it’s making sure your billing team knows the wind-down is coming, how long it lasts, and what they’re responsible for in both systems.

The handoff you didn’t know was coming

Somewhere around 30 to 60 days after go-live, your EHR vendor transitions you from the project manager who handled your implementation to a customer success manager who handles your ongoing relationship.

It makes sense from the vendor’s side because the PM’s job is done once you’re live, and a different person takes over for the long term.

But from your side, it feels abrupt. The person who knew your setup, your history, and your specific configuration is gone. The new contact is starting from scratch on understanding your practice. And this transition is happening right in the middle of everything else: clinical data still converting, billing still running in two systems, your team still getting comfortable with the new platform.

We see this create confusion on almost every transition. The practice has a question about something that was decided during implementation, and the CSM doesn’t have the context. Or the practice assumes the CSM knows about a customization the PM set up, and they don’t. The handoff is usually smooth on the vendor’s end, but on the practice’s end it feels like losing your guide halfway through the trail.

The best thing you can do is document your implementation decisions and any custom configurations before the PM leaves. Don’t rely on the handoff to carry that context. Have it written down on your side so you can bring the new contact up to speed instead of waiting for them to figure it out.

It also helps to understand what the CSM relationship looks like going forward, because it’s fundamentally different from what you had with the PM. Your PM was focused on getting you live. They were in the details of your configuration, your timeline, your specific setup decisions. Your CSM is managing an ongoing relationship across many accounts, so they’re not going to have that same depth of context about your practice. They’re there for support requests, renewals, and escalations, not for the hands-on guidance you had during implementation. Adjusting your expectations for that shift early makes the transition less frustrating for both sides.

The questions nobody asked during the sales process

Once the EHR transition is complete and the dust starts to settle, a different set of questions tends to surface. These aren’t about the EHR. They’re about the IT, security, and infrastructure around it that nobody brought up during the sales process.

• Who’s managing our network and infrastructure now? The EHR vendor built the software, not your network. If your practice changed systems, there may be infrastructure that needs to be updated, reconfigured, or supported differently.
• Is our security posture current? An EHR transition often reveals gaps in security: permissions that were set up quickly during implementation, access controls that haven’t been reviewed, compliance documentation that needs updating.
• How do we get reporting across our old and new systems? During the wind-down period, your data lives in two places. Leadership wants a unified view of operations and revenue cycle, and the new EHR may not have the reporting configured the way you need it yet.
• What happened to our third-party connections? Data feeds, lab integrations, clearinghouse connections, anything that was wired into your old system may need to be rebuilt or reconnected in the new environment.
• What about the data from our old system long term? Once the conversion is complete and the legacy licenses expire, where does that historical data live? Is it accessible? Who maintains it?

These are real questions that come up on almost every transition we’re part of. And they tend to come up after the EHR vendor considers their job done, which means the practice is on their own to figure out who handles them.

Here’s what this typically looks like. You’re about two months post-go-live. The clinical data has landed. Your team is getting comfortable with the new system. And then your office manager mentions that the network has been slow since the switch, or your practice administrator realizes nobody has reviewed the access permissions that were set up during implementation, or leadership asks for a report that requires pulling from the old system and the new one at the same time and nobody knows how to do it.

These aren’t emergencies, but they’re problems that need someone to own them, and the EHR vendor isn’t the answer because it’s not their layer.

What to keep track of during the first 90 days

This isn’t a comprehensive project plan, but it’s the short list of things we’d tell any practice to stay on top of:

• Clinical conversion status: when was the data extracted, when did we receive it, what’s the estimated completion date
• Billing wind-down progress: how much is left in the old system’s pipeline, who’s responsible for working it down, when do you expect to be fully transitioned
• Legacy system access: are your licenses or read-only access confirmed through the full 90 to 120 day window
• EHR vendor handoff: who is your new ongoing contact, when does the handoff happen, what documentation do you need to preserve from the implementation
• Third-party connections: which integrations from the old system have been reconnected in the new one, which ones are still pending
• IT and security review: has anyone looked at your network, permissions, and compliance documentation since the transition
• Reporting: can leadership get the data they need across both systems during the wind-down, and is the new system’s reporting configured the way you need it

You don’t need to manage all of this alone. But you do need to know it’s happening, because the overlap is where things get missed.

Where Focus comes in

The conversion is usually how a practice first works with us. But the first 90 days after go-live are where the relationship either ends or expands, depending on what surfaces.

We handle the data conversion piece: the clinical data moving in the background, the demographic and appointment data that converted before go-live, and any non-standard work that comes up along the way. We’ve done more than 2,000 of these across 100-plus EHR systems, and we’ve never missed a go-live.

But once the transition dust settles and the questions about IT, security, and reporting start coming up, those are conversations we have every day with practices just like yours. A lot of the groups we work with started with us on a conversion and then realized the IT infrastructure, security, and data questions that surfaced afterward were things we could help with too.

As your Unified Partner, we handle IT, security, and data together. The conversion is often just the beginning.

If you’re in the middle of a transition right now, or you’re about to start one, and you want to know what the next 90 days are going to look like, that’s a conversation we’re happy to have.

Frequently asked questions

What happens after you go live on a new EHR?

Your clinical data converts in the background over six to eight weeks. Your billing runs in two systems during a 90 to 120 day wind-down. Your EHR vendor transitions you from your implementation PM to an ongoing support contact. And the questions about IT, security, and reporting that weren’t part of the sales conversation start surfacing. All of this happens simultaneously.

How long does the billing wind-down take?

Typically 90 to 120 days after go-live. During that period, new visits bill out of your new system while everything already in the pipeline stays in the old one and gets worked down over time. Your billing team needs to know this is coming well before go-live.

What is the PM-to-CSM handoff?

Around 30 to 60 days after go-live, your EHR vendor transitions you from the project manager who handled your implementation to a customer success manager for ongoing support. The PM’s job is considered complete once you’re live. Document your implementation decisions and custom configurations before that handoff happens so you’re not relying on it to carry context.

What should I be tracking during the first 90 days?

Clinical conversion status, billing wind-down progress, legacy system access confirmation, the EHR vendor handoff timeline, third-party reconnections, and whether anyone has reviewed your IT infrastructure and security posture since the transition. The overlap between all of these is where things get missed.

Does Focus stay involved after the data conversion is complete?

The conversion is often the first time a practice works with us, but it doesn’t have to be the last. Once the EHR transition reveals the IT, security, and reporting questions that weren’t part of the original conversation, those are things we help practices with every day. As your Unified Partner, we handle IT, security, and data together.