Payroll that already knows what your clinicians billed.
Run payroll inside the same system your team documents and bills in. Salary, hourly, per service code, productivity, commission, or 1099, PIMSY calculates it from the services your providers have already posted.
When pay lives outside the EHR, every pay period is a rebuild.
Behavioral health practices rarely pay everyone the same way. One clinician is on a percentage of what they bill, another is salaried, a contractor is 1099 on commission, and the front desk is hourly. Pull all of that into a spreadsheet and someone spends the period end exporting service reports, cross-checking units, applying each person’s rate by hand, and hoping nothing was missed.
It gets harder when billing moves after the fact. A payer denies a claim or recoups a payment, and the commission already paid on that service is now wrong. Tracking those adjustments by hand is slow, and the errors are the kind that erode trust with your providers.
PIMSY closes that gap by keeping payroll in the same record as scheduling, documentation, and billing. The services your clinicians post are the same data payroll calculates from, so a pay run is a review step, not a rebuild.
What behavioral health teams actually need from payroll
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Flexible pay structures: percentage based, flat rates, hourly, and per service code in one run -
Productivity-based calculations drawn straight from posted services, not re-keyed totals
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Automatic adjustments when a payer recoups a payment or reverses a denial
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Automated accruals each pay period, including PTO and vacation, plus mileage tracking
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HIPAA-compliant reports that exclude PHI and show each employee only what they should see
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A clean gross-pay export to QuickBooks, Paychex, or other payroll software
From posted services to an approved run
Set each person’s pay rules once, then let every period calculate itself from the work already in the chart.
Set pay structures and schedules
Assign each team member a pay structure: percentage based, flat rate, per service code, productivity, hourly, or 1099 commission. Set pay periods to weekly, bi-weekly, monthly, or a custom cadence, and organize pay by user group, location, or individual.
PIMSY calculates from posted services
When the period closes, payroll pulls the services your clinicians have posted and applies each pay rule to them. Productivity and percentage figures come from real billed work, accruals for PTO and vacation are applied automatically, and recoupments or reversed denials are accounted for.
Review, then export the gross
Review a transaction breakdown for each employee and a global overview of historical runs. Reports exclude PHI and can be limited to what each person should see. Export the gross to QuickBooks, Paychex, or other payroll software for withholdings and benefits.
Payroll is one part of PIMSY
Pay is calculated from billing, billing comes from documentation, and documentation comes from the schedule. It all runs inside PIMSY, with the patient record at the center.
What practices say about running on PIMSY
We recently went through our first CARF International survey and, yesterday, we received great news that we are now CARF accredited. It required developing policy and procedure manuals, the employee handbook, and investing and implementing SaaS in Payroll/HR, LMS and EHR, as well as HIPAA compliant, business class office suite (M 365) and networks. Thanks to the PIMSY team for implementing PIMSY as our Electronic Health Record!
PIMSY is a very robust program that is adaptable to all agency sizes. Once you get to know PIMSY, you’ll wonder how you kept track of anything before it.
Questions about payroll in PIMSY
If a payer adjusts or recoups payments, will the administrator be alerted?
Yes. If a payer recoups a service, the payroll module automatically adjusts the next payroll, reducing administrative workload. If a payer reverses a denial and makes a payment, PIMSY accounts for it, ensuring accurate compensation for commission-based providers.
Can I control what payroll information employees see?
Yes. PIMSY allows you to customize payroll report settings, ensuring employees only see the relevant details. Reports are available for staff review and exclude PHI to keep them compliant.
How does PIMSY handle payroll adjustments for billing changes or service denials?
PIMSY EHR’s Payroll feature automatically adjusts payroll based on service denials, payer recoupments, and billing changes. This reduces administrative workload and ensures payroll accuracy without a manual rebuild each time billing moves.
Does PIMSY’s Payroll feature handle tax withholdings and benefits calculations?
No, PIMSY calculates payroll up to the gross amount. Payroll reports can be exported to QuickBooks or other payroll software for tax withholdings and benefits management. Ask us about our new integration with Paychex.
What pay structures and schedules does PIMSY support?
PIMSY calculates payroll based on each employee’s specific pay structure, including percentage based, flat rates, hourly, per service code, productivity, commission, and 1099, as well as nonbillable time like training and staff meetings. Pay periods can be weekly, bi-weekly, monthly, or custom, organized by user group, location, or individual.
Does PIMSY track PTO, accruals, and mileage?
Yes. PIMSY automates accrual calculations per pay period, including PTO and vacation, and includes mileage and PTO calculations. Detailed payroll history is maintained for each team member, with a global overview of historical transactions for review.
Payroll processing that keeps pay tied to the work in the chart.
Book a free demo to see how PIMSY runs behavioral health payroll inside the clinical workflow, from flexible pay structures and automated accruals to HIPAA-compliant reports and a clean export to QuickBooks or Paychex.
- Salary, hourly, per service, productivity, commission, and 1099 in one run
- Productivity-based calculations drawn from posted services
- Automated PTO, vacation, and mileage accruals
- HIPAA-compliant reports that exclude PHI
- Gross export to QuickBooks, Paychex, or other payroll software
Book a Free Demo