How to Switch EHRs Without Losing Patient Records: Complete 2026 Guide

Step-by-step guide to switching EHR systems safely. Learn how to export data, avoid common pitfalls, and transition smoothly without disrupting your practice or losing patient information.

By ClinikEHR Team

January 25, 2026

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20 MINS

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You've decided to switch EHR systems. Maybe your current system is too expensive, too limited, or just too frustrating. But now you're facing the big question: How do I move all my patient data without losing anything or disrupting my practice?

The good news: switching EHRs is much easier in 2026 than it was even a few years ago. With the right approach, you can transition smoothly in 4-6 weeks without losing data or missing appointments. This guide walks you through every step.

Quick Answer

Switching EHRs safely requires a systematic 6-8 week process: Export all data from your current EHR (demographics, notes, financial data, documents) in Week 3. Set up your new EHR and customize templates in Week 4. Import your data in Week 5 (ClinikEHR offers free migration assistance). Run both systems in parallel for 1-2 weeks to ensure nothing is missed. Fully transition in Week 7+. Most critical: export more than you think you need, keep your old EHR active for 30-60 days as backup, and choose an EHR like ClinikEHR that never charges data export fees. The actual work is 15-25 hours spread over 6-8 weeks. ClinikEHR accepts all standard formats (CSV, PDF, CCD/CCDA) and provides free import assistance on all paid plans.

Smooth EHR Migration

ClinikEHR offers free data migration assistance. We accept all formats and help you import everything safely.

Learn About Migration

When to Switch EHRs

Before diving into the how, let's confirm you're switching for the right reasons:

Good Reasons to Switch

✅ Cost: Your current EHR costs 2-3x more than alternatives with similar features

✅ Missing Features: You need features your current EHR doesn't offer (AI notes, telehealth, better reporting)

✅ Poor Support: Your vendor doesn't respond to issues or help requests

✅ Usability Issues: Your EHR is clunky, slow, or frustrating to use daily

✅ Growth Limitations: Your practice has outgrown your current system's capabilities

✅ Vendor Instability: Your EHR company is struggling financially or being acquired

✅ Compliance Concerns: Your current system doesn't meet regulatory requirements

Bad Reasons to Switch

❌ Minor Frustrations: Every EHR has quirks. Don't switch over small annoyances.

❌ Grass is Greener: The new system will have its own learning curve and limitations.

❌ Impulse Decision: Switching takes time and effort. Make sure it's worth it.

❌ Without Research: Don't switch without thoroughly testing the new system first.

Bottom Line: If your current EHR is costing you significant time or money, switching makes sense. If it's just mildly annoying, you might want to stick it out.

What You Can (and Can't) Export

Understanding what data you can export is crucial for planning your migration:

Data You Can Usually Export

✅ Patient Demographics

Names, dates of birth, contact information
Insurance information
Emergency contacts
Usually exports as CSV or Excel

✅ Appointment History

Past and future appointments
Appointment types and durations
Usually exports as CSV

✅ Financial Data

Invoices and payments
Outstanding balances
Transaction history
Usually exports as CSV

✅ Documents

Uploaded PDFs, images, forms
Usually downloadable individually or in bulk

✅ Clinical Notes (with limitations)

Often export as PDFs (not editable)
Some systems export as structured data (CCD/CCDA format)
Quality varies by vendor

Data That's Often Difficult to Export

⚠️ Structured Clinical Data

Many EHRs export notes as PDFs, not structured data
Treatment plans may not export in usable format
Custom fields often don't transfer

⚠️ Templates and Customizations

Your custom note templates usually don't export
Workflow customizations need to be recreated
Macros and shortcuts don't transfer

⚠️ Integrations

Third-party integrations need to be set up again
API connections don't transfer

⚠️ Historical Billing Data

Some systems limit how far back you can export
Claim history may be incomplete

Data You Probably Can't Export

❌ System Configurations

User permissions and roles
Appointment type settings
Fee schedules
Email templates

❌ Portal Messages

Historical patient portal communications
Secure messages

❌ Audit Logs

Who accessed what and when
System activity history

Key Takeaway: You can export most important data, but expect to lose some historical details and need to recreate customizations.

Step-by-Step Migration Process

Here's the complete timeline and process for switching EHRs:

Phase 1: Planning (Weeks 1-2)

Week 1: Research and Selection

Day 1-2: Identify Requirements

List must-have features
Identify deal-breakers
Set budget constraints
Consider growth needs

Day 3-4: Research Options

Read reviews and comparisons
Watch demo videos
Check pricing carefully
Verify HIPAA compliance

Day 5-7: Test Top Candidates

Sign up for free trials
Test with real workflows
Have staff test if applicable
Compare side-by-side

ClinikEHR Advantage: Free-forever plan lets you test thoroughly without time pressure or credit card.

Week 2: Decision and Preparation

Day 1-2: Make Final Decision

Choose your new EHR
Review contract carefully
Understand data import process
Confirm support availability

Day 3-4: Review Current Data

Identify what needs to be exported
Clean up duplicate or outdated records
Archive inactive patients
Document custom workflows

Day 5-7: Plan Timeline

Choose switch date (avoid busy periods)
Notify staff of upcoming change
Block time for training
Plan for running both systems temporarily

Phase 2: Data Export (Week 3)

Export Checklist:

Day 1: Patient Demographics

Log into current EHR
Navigate to export/reports section
Export all patient data as CSV
Verify export includes:
- Full names
- Dates of birth
- Contact information (phone, email, address)
- Insurance information
- Emergency contacts
- Medical record numbers

Day 2: Appointment History

Export past appointments (last 12-24 months)
Export future appointments
Verify export includes:
- Patient names
- Appointment dates and times
- Appointment types
- Provider names
- Status (completed, cancelled, no-show)

Day 3: Clinical Notes

Determine export format (PDF vs structured data)
Export notes by patient or date range
Organize exported files logically
Verify completeness

Options:

PDF Export: Download all notes as PDFs (time-consuming but complete)
Structured Export: Request CCD/CCDA files if available (better for import)
Selective Export: Export only recent notes (last 6-12 months) for active patients

Day 4: Financial Data

Export invoice history
Export payment transactions
Export outstanding balances
Verify totals match your records

Day 5: Documents and Files

Download uploaded documents
Organize by patient
Verify file integrity
Create backup copies

Day 6-7: Backup and Verify

Create complete backup of all exported data
Store backup in multiple locations (cloud + local)
Verify all files are readable
Document what was exported and what wasn't

Pro Tip: Export more than you think you need. It's easier to have extra data than to go back and export again later.

Phase 3: New EHR Setup (Week 4)

Setup Checklist:

Day 1-2: Basic Configuration

Create provider profile(s)
Set up practice information
Configure appointment types
Set up fee schedule
Configure payment processing

Day 3-4: Customization

Create note templates
Set up intake forms
Configure consent forms
Customize email templates
Set up automated reminders

Day 5: Patient Portal Setup

Customize portal branding
Configure online booking
Set up patient-facing forms
Test booking process
Create welcome email template

Day 6-7: Integration and Testing

Add booking widget to website
Set up email integration
Configure calendar sync
Test all workflows
Train staff on new system

ClinikEHR Advantage: Setup wizard walks you through everything in 30-60 minutes. Free migration assistance on paid plans.

Phase 4: Data Import (Week 5)

Import Process:

Day 1-2: Import Patient Demographics

ClinikEHR Process:

Go to Settings → Import Data
Upload CSV file
Map fields (name → name, email → email, etc.)
Review mapping
Click "Import"
Verify import completed successfully

Common Issues:

Date format mismatches (fix in Excel before importing)
Phone number formatting (remove special characters)
Duplicate records (merge or delete)

Day 3-4: Upload Clinical Notes

Option 1: PDF Upload (Recommended for Historical Notes)

Go to each patient profile
Upload PDF notes to documents section
Label clearly (e.g., "Notes 2020-2025 from [Old EHR]")
Patients can access via portal if needed

Option 2: Manual Re-entry (Recommended for Active Patients)

For active patients, manually re-enter recent notes
Use new EHR's note format
Reference old PDFs as needed
Provides cleaner, more usable data

Option 3: Structured Import (If Available)

Upload CCD/CCDA files
System automatically parses clinical data
Review and verify accuracy
Best option if your old EHR supports it

Day 5: Import Financial Data

Upload transaction CSV
Map fields
Verify balances match
Reconcile any discrepancies

Day 6: Upload Documents

Drag and drop documents to patient profiles
Organize by category
Verify all files uploaded correctly

Day 7: Final Verification

Spot-check 10-20 patient records
Verify all critical data imported
Test workflows end-to-end
Document any issues

Phase 5: Parallel Operation (Week 6)

Running Both Systems:

Why Run Both Systems?

Reduces risk of data loss
Gives you time to adjust
Allows reference to old system
Provides safety net

How to Do It:

New Appointments: Schedule in new EHR only
New Notes: Write in new EHR only
Historical Reference: Keep old EHR open (read-only)
Billing: Use new EHR for new transactions
Patient Portal: Transition patients to new portal

Week 6 Schedule:

Day 1-2: Start using new EHR for all new work
Day 3-4: Reference old EHR as needed
Day 5-6: Gradually stop using old EHR
Day 7: Fully transition to new EHR

Troubleshooting:

Keep old EHR login handy for first 2-4 weeks
Document any issues or missing data
Contact new EHR support for help
Don't cancel old EHR until confident

Phase 6: Full Transition (Week 7+)

Final Steps:

Week 7: Verify Everything Works

Test all workflows thoroughly
Ensure staff is comfortable
Verify patient portal works
Check billing processes
Confirm reporting works

Week 8: Cancel Old EHR

Before Canceling:

Export final backup from old system
Verify all data is in new system
Download any remaining documents
Save final backup to secure storage (keep for 7-10 years)
Document what was exported and where it's stored

Cancellation Process:

Contact old EHR vendor
Request cancellation
Confirm no early termination fees
Request final data export (if not done already)
Verify account is closed
Keep confirmation email

Week 9+: Optimize New System

Refine workflows based on experience
Add additional customizations
Train staff on advanced features
Gather feedback and adjust

Common Pitfalls and How to Avoid Them

Pitfall #1: Not Exporting Enough Data

The Problem: You export basic demographics but forget appointment history, financial data, or documents. Later, you need this information and can't access it.

The Solution: Export everything, even if you're not sure you'll need it. Storage is cheap; re-exporting is time-consuming.

Checklist:

✅ Patient demographics
✅ Appointment history (past and future)
✅ Clinical notes (all formats available)
✅ Treatment plans
✅ Financial data (invoices, payments, balances)
✅ Documents (PDFs, images, forms)
✅ Insurance information
✅ Medication lists
✅ Allergy information

Pitfall #2: Switching During Busy Season

The Problem: You switch EHRs during your busiest time of year, causing stress and errors.

The Solution: Choose a slow period for your practice. For most practices, this is:

Summer (July-August)
Late December/early January
Any period with fewer appointments

Avoid:

Back-to-school season (September)
Tax season (March-April for some practices)
Holiday season (November-December for retail-focused practices)

Pitfall #3: Not Testing Thoroughly

The Problem: You switch without fully testing the new EHR, then discover critical features don't work as expected.

The Solution: Test everything during your trial period:

Write 10-20 practice notes
Schedule mock appointments
Process test payments
Send test patient portal invitations
Generate reports
Test on mobile devices

ClinikEHR Advantage: Free-forever plan lets you test as long as you need without time pressure.

Pitfall #4: Not Training Staff

The Problem: You learn the new system but don't train your staff, causing confusion and errors.

The Solution:

Schedule training sessions for all staff
Create quick reference guides
Practice with test patients
Allow time for questions
Be patient during adjustment period

Pitfall #5: Canceling Old EHR Too Soon

The Problem: You cancel your old EHR immediately, then realize you need to reference historical data.

The Solution: Keep your old EHR active for 30-60 days after switching. The extra month or two of cost is worth the peace of mind.

Pitfall #6: Not Documenting the Process

The Problem: You don't document what was exported, where it's stored, or how to access it later.

The Solution: Create a migration document that includes:

What data was exported
Export dates
File locations
Backup locations
Any data that couldn't be exported
Contact information for old EHR vendor
Notes about the migration process

Why ClinikEHR Makes Switching Easy

After helping hundreds of practices switch EHRs, we've built ClinikEHR to make migration as painless as possible:

Free Migration Assistance

What We Provide:

Step-by-step migration guide
Data import templates
Field mapping assistance
Troubleshooting support
Training resources

Available On:

All paid plans (Starter, Professional, Practice)
Free plan includes self-service resources

Flexible Import Options

We Accept:

CSV files (demographics, appointments, financial data)
PDF documents (notes, forms, images)
CCD/CCDA files (structured clinical data)
Excel spreadsheets
Most common export formats

We Help With:

Field mapping
Data cleaning
Duplicate detection
Format conversion

No Data Export Fees

The Promise: If you ever decide to leave ClinikEHR, we'll help you export all your data at no charge. No fees, no hassle, no vendor lock-in.

What You Can Export:

All patient data (CSV)
All clinical notes (PDF and structured formats)
All documents
All financial data
Complete backup of your account

Why This Matters: Many EHRs charge $500-2,000 for data export or make it intentionally difficult. We believe your data is yours, and you should be able to take it with you anytime.

Smooth Transition Process

Week 1-2: Planning

Sign up for free plan or trial
Test thoroughly with real workflows
Decide if ClinikEHR is right for you

Week 3: Export from Old EHR

Follow our export guide
We provide templates and checklists

Week 4: Setup ClinikEHR

Use our setup wizard (30-60 minutes)
Customize templates and forms
Configure integrations

Week 5: Import Data

Upload CSV files (we help with mapping)
Upload documents
Verify everything imported correctly

Week 6: Parallel Operation

Use ClinikEHR for new work
Reference old EHR as needed
Adjust workflows

Week 7+: Full Transition

Cancel old EHR
Optimize ClinikEHR
Enjoy better features at lower cost

Real Migration Success Stories

Case Study 1: Sarah, LMFT (SimplePractice → ClinikEHR)

Background:

35 clients
3 years of data in SimplePractice
Frustrated by cost ($708/year) and lack of AI features

Migration Timeline:

Week 1: Tested ClinikEHR free plan
Week 2: Exported data from SimplePractice
Week 3: Set up ClinikEHR, imported demographics
Week 4: Uploaded recent notes, ran both systems
Week 5: Fully transitioned to ClinikEHR

Results:

Saved $360/year (ClinikEHR Professional vs SimplePractice Plus)
AI notes save 3 hours/week
No data lost
Smoother than expected

Quote: "I was nervous about switching, but ClinikEHR's migration guide made it straightforward. The hardest part was exporting notes from SimplePractice—everything else was easy."

Case Study 2: Dr. Michael Chen, Psychiatrist (TherapyNotes → ClinikEHR)

Background:

50 patients
5 years of data in TherapyNotes
Wanted AI documentation and lower cost

Migration Timeline:

Week 1-2: Tested ClinikEHR Professional plan
Week 3: Exported all data from TherapyNotes
Week 4: Set up ClinikEHR, imported demographics
Week 5: Uploaded documents, imported financial data
Week 6: Ran both systems in parallel
Week 7: Fully transitioned

Results:

Saved $480/year (ClinikEHR Professional vs TherapyNotes Professional)
AI notes save 4 hours/week
All data successfully migrated
Staff adapted quickly

Quote: "The migration took about 15 hours of my time over 6 weeks. The AI notes alone save me that much time in a month. Best decision I've made for my practice."

Frequently Asked Questions

How long does it take to switch EHRs? Plan for 6-8 weeks from decision to full transition. The actual work is 15-25 hours spread over that time. Most practices run both systems in parallel for 1-2 weeks before fully switching.

Will I lose any patient data when switching? You shouldn't lose any critical data if you export properly. However, some historical details (old portal messages, audit logs) may not transfer. Clinical notes, demographics, and financial data should all export successfully.

Can I switch EHRs without disrupting my practice? Yes. By running both systems in parallel for 1-2 weeks, you can transition smoothly without missing appointments or losing data. Choose a slow period for your practice to minimize stress.

How much does it cost to switch EHRs? The main costs are your time (15-25 hours) and potentially one extra month of your old EHR subscription. Some EHRs charge data export fees ($500-2,000), but ClinikEHR never charges for data export.

What if my current EHR won't let me export data? By law (21st Century Cures Act), EHR vendors must provide data export capabilities. If your vendor refuses, contact them in writing and reference the law. If they still refuse, file a complaint with ONC (Office of the National Coordinator for Health IT).

Do I need technical skills to switch EHRs? No. If you can use Excel and follow step-by-step instructions, you can switch EHRs. ClinikEHR provides detailed guides and support to help you through the process.

Should I hire someone to help with EHR migration? For most solo practitioners and small practices, you can do it yourself with vendor support. For larger practices (5+ providers) or complex setups, hiring a consultant might save time.

What's the best time of year to switch EHRs? Choose a slow period for your practice—typically summer (July-August) or late December/early January. Avoid busy seasons and major holidays.

Conclusion: Switch with Confidence

Switching EHR systems is a big decision, but it doesn't have to be scary. With proper planning, the right tools, and a systematic approach, you can transition smoothly in 6-8 weeks without losing data or disrupting your practice.

The Key Steps:

Export all data from your current EHR (Week 3)
Set up your new EHR (Week 4)
Import your data (Week 5)
Run both systems in parallel (Week 6)
Fully transition (Week 7+)

ClinikEHR Makes It Easy:

Free migration assistance on all paid plans
Accepts all common export formats
No data export fees (ever)
Smooth import process
Excellent support throughout

Ready to Make the Switch?

Start Free with ClinikEHR — Test thoroughly with our free-forever plan before committing. No credit card required, no time limit.

Need help planning your migration? Contact our team — We'll walk you through the process and answer all your questions.

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