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Run the Payroll Fee Auditor →Blog · Payroll Management · Healthcare
Healthcare Practices: Payroll Software vs. Managed Payroll Service (2026)
Healthcare practices evaluating payroll options typically compare managed payroll service against payroll software. Here is the honest comparison.
Managed payroll service (like BEG) means a provider processes payroll for you. You submit hours and changes; they handle the rest including tax deposits, compliance, and year-end forms.
Payroll software (Gusto, ADP Run, Paychex Flex) means you run payroll yourself using a platform. You are responsible for configuring it correctly and keeping up with compliance changes.
Side-by-Side Comparison for Healthcare Practices
| Payroll Task | Managed Payroll | DIY Software |
|---|---|---|
| Shift differentials setup | Configured for you | You configure |
| Tax deposits | Handled | You are responsible |
| Compliance updates | Applied automatically | Your responsibility |
| Multi-state filing | Included | Varies by plan |
| Year-end W-2s | Included | Included or add-on |
| Payroll errors | Provider corrects at cost | Your cost to fix |
| New hire onboarding | Handled | You set up |
Which Is Right for Healthcare Practices?
For most healthcare practices under 100 employees, managed payroll wins on total cost and compliance coverage. The tradeoff -- giving up direct software access -- is outweighed by removing the compliance risk that comes with self-managing shift differentials, on-call pay, credentialing-based pay tiers, multi-location clinic payroll.
Payroll software makes sense if you have dedicated in-house HR staff with genuine expertise in Healthcare Practices payroll compliance, prefer hands-on control, and have a low tolerance for vendor dependency. These are real advantages, but they come with real responsibility.
Managed Payroll, Handled.
BEG manages payroll at $25-$45 per employee per month, all-inclusive. Get an instant cost comparison for your business.
Frequently Asked Questions
Can you handle shift differentials for nurses?
Yes. Shift differentials are set up as pay rate modifiers. Night shift, weekend, and on-call differentials apply automatically based on hours worked, producing the correct blended rate and overtime calculation.
How do you handle ACA reporting?
For practices with 50 or more full-time equivalent employees, we handle Form 1094-C and 1095-C preparation and filing. We track hours to determine ACA full-time status and flag coverage gaps.
Can you process payroll for multiple clinic locations?
Yes. Multi-location practices run on a single payroll system with consolidated reporting and per-location cost center codes.
How do you handle credentialing-based pay tiers?
Credentialing-based tiers are configured as pay grade structures. When a provider advances, the pay tier updates on the date you specify.
What does BEG charge for healthcare payroll?
Healthcare payroll runs at $25-$45 per employee per month, all-inclusive. For a 25-person practice, that is $625-$1,125 per month.
Related Resources
Anthony leads payroll solutions at Business Executive Group, a national managed payroll firm serving businesses across industries including Healthcare Practices. BEG manages payroll at $25-$45 PEPM, all-inclusive, with deep expertise in compliance, multi-state filing, and industry-specific payroll requirements. Get instant pricing at beghr.com.
Authoritative source: U.S. Department of Labor: Wage and Hour Division
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