Bookkeeping, payroll, and tax for independent healthcare practices, from a Kansas City firm trusted since 1995.

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Clinician Pay

Session-based clinician pay calculated every pay run, following the practice's existing compensation agreements, so clinicians are paid correctly and on time.

What This Is

Most behavioral health groups and therapy practices pay clinicians by the session, the visit, or the unit. A therapist might earn one rate for an intake and another for a standard 53-minute session. A physical therapist might be paid differently for an evaluation than for a follow-up visit. Some agreements pay on what was billed and others on what was actually collected. Some add a base salary or a draw on top. Each clinician’s agreement is often a little different from the next.

This service takes the compensation agreements you already have and applies them to every pay run. We pull session counts from your practice management reports, calculate what each clinician is owed, and run the payroll in Gusto. We don’t write or recommend pay structures. How clinicians are paid is subject to Stark Law and other healthcare compliance rules, so those decisions stay with you and your attorney. Our job is to apply the terms you’ve already agreed to, accurately and on time.

The Work

Review each clinician’s agreement and set up the rates, tiers, and rules it contains. Check session reports against the schedule to catch missing or duplicate entries. Apply no-show, late cancellation, and session length rules exactly as each agreement describes them. Run payroll for W-2 clinicians, payments for contractors, and pay for your front desk and admin staff.

What We Need From You

A signed compensation agreement for each clinician, plus any updates when terms change. Session or visit reports from your practice management system each pay period. Collections data if any agreements pay on what was collected. A quick review and approval before payroll goes out.

Why This Matters

For most owners of these practices, paying clinicians correctly is the biggest money problem they have. It’s usually the largest expense, and it’s often calculated by hand in a spreadsheet only one person understands. Every pay period someone exports a report, sorts sessions by clinician, checks codes, and multiplies rates. A missed late cancel or a miscounted session doesn’t seem like much in a single pay period. Over a year it adds up for both the practice and the clinician.

The cost isn’t only financial. Clinicians notice when a check is short, and they notice faster when it happens twice. A pay dispute can damage a working relationship that took months to build, and good clinicians are hard to find. Marcella Nichols, the firm’s President, holds a master’s degree in clinical psychology and spent seven years in recruiting and HR. She understands how these practices work and how quickly trust wears down when people aren’t paid what they expected.

Spreadsheet Risk

Formulas break. Copied rows get skipped. A rate change gets entered for one clinician but not carried forward the next month. When the person who built the spreadsheet is out sick or leaves the practice, nobody else knows how it works and payroll gets delayed or estimated.

Owner Time

Owners who also carry a caseload end up doing pay calculations at night after a full day of sessions. Every hour spent reconciling session counts is an hour not spent seeing clients, supervising staff, or running the practice.

What Changes

Every pay run, clinicians receive pay that matches their agreements, with a clear breakdown of the sessions and rates behind the total. If a clinician asks how their check was calculated, there’s an answer that traces back to the session report and the agreement itself. You review and approve the numbers instead of building them from scratch.

When you hire a new clinician or change someone’s terms, you send the updated agreement and the new rates take effect on the next pay run. The same team handles your payroll, and often your bookkeeping as well, so clinician pay lines up with the rest of your financial records. You’re working with enrolled agents who know your practice, not a support line.

Fewer Pay Disputes

Consistent calculations and clear pay statements mean fewer questions and fewer uncomfortable conversations with your clinicians. When a question does come up, there’s a record showing exactly how the number was reached, which usually settles it quickly.

Payroll That Holds Up

Clinician pay, staff pay, payroll taxes, and year-end W-2s and 1099s all run through one system, in any state where you have clinicians. If a past check is ever questioned or reviewed, the calculations and source reports are organized and easy to find.

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Baker's Bookkeeping & Tax Services has handled bookkeeping, payroll, and tax work from Lenexa, Kansas, since 1995. Today we serve independent medical and healthcare practices nationwide, with tax work and IRS notices handled by credentialed enrolled agents. We prepare around 1,000 returns a year, and most of our clients are families who have trusted us for two or three generations.

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