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

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Therapy & Rehab Practices

Physical therapy, OT, speech, and chiropractic practices pay clinicians by productivity. We calculate that pay from your agreements and check collections against the bank.

The Industry

A physical therapy practice with four clinicians reaches the end of a pay period. The owner exports visit counts from the billing system and separates evaluations from follow-ups. Then she checks the agreements to see whether a late cancellation counts toward the bonus threshold and works out four different paychecks by hand. It takes most of Sunday. On Tuesday one of the PTAs asks why her check is $180 lower than she expected. The owner can’t say for sure whether the math was wrong or the visit count was wrong.

There are about 39,000 outpatient physical therapy clinics and 40,000 chiropractic offices in the US, plus thousands of occupational and speech therapy practices. Most of them pay clinicians by productivity. That might be per visit, per unit, a percentage of collections, or a base salary with a bonus once a visit target is met. Every one of those depends on numbers from the billing system. The money behind those numbers arrives weeks or months later from Medicare, commercial plans, Medicaid, workers’ comp, and auto insurers. The pay and the collections have to agree, and in most practices nobody is checking that they do.

Who This Covers

Outpatient physical therapy clinics, occupational therapy practices, pediatric and adult speech therapy practices, and chiropractic offices. Practices with a few clinicians up to multi-location groups, with PTs, PTAs, OTs, COTAs, SLPs, chiropractors, massage therapists, aides, and front-desk staff on payroll. We work with practices anywhere in the country.

What Makes It Complex

Clinician pay tied to visits, units, or collections. Different rates for evaluations, re-evaluations, and follow-ups. Cancellations and no-shows that may or may not count, depending on the agreement. Insurance payments that cover dozens of patients in one deposit and sometimes subtract takebacks from older claims. Workers’ comp and personal injury cases that take months to pay. Clinics in more than one state.

What We Handle

We calculate clinician pay every pay run using the compensation agreements you already have. You send the agreements once and the productivity reports from your billing system each period. We apply the terms as written, including rate differences, bonus thresholds, and how cancellations are treated, and the results go straight into payroll. We don’t design or recommend pay plans. Clinician compensation in healthcare falls under Stark Law and other compliance rules, so those decisions stay with you and your healthcare attorney. Our job is to make sure the agreements you signed are followed accurately every time.

Your books are kept in QuickBooks Online and closed every month with a one-page summary. Each month we compare what your billing system says was collected against what actually reached the bank. If the books are behind when we start, we bring them current first. This is the same work we already do for behavioral health groups, where clinicians are also paid per session, so the process is tested and ready for your practice.

Clinician Pay Every Pay Run

Per visit, per unit, a percentage of collections, or a base plus a productivity bonus. Whatever your agreements say, we apply it the same way every period and keep a record of how each check was figured. When a clinician asks about their pay, you have the visit counts, the rate, and the math in front of you.

Payroll and Collections Checks

Payroll for clinicians, aides, and front-desk staff runs through Gusto in any state. That matters for a practice with clinics in both Kansas and Missouri or a speech therapist working remotely from another state. Monthly bookkeeping matches insurance collections to bank deposits, so the collections figure behind clinician pay is one you can rely on.

Common Problems

The billing system says the practice collected $86,000 last month. Insurance deposits in the bank add up to $81,400. The difference could be a Medicaid payment posted to the wrong month. It could be a commercial payer taking back an overpayment from last spring out of this month’s check. It could be a payment that was posted but never deposited. If clinicians are paid a percentage of collections, a gap like that goes straight into payroll. Someone gets paid on money that never arrived, or doesn’t get paid on money that did.

Pay calculated by hand tends to drift over time. The owner or office manager builds a spreadsheet. A new clinician joins on slightly different terms, a rate changes in January, and the old formula keeps running anyway. Cancellations get counted one way this month and another way next month. The errors are small one at a time but they add up over a year, and every correction is an awkward conversation. Good clinicians are hard to find, and repeated pay mistakes are one of the fastest ways to lose one.

Pay Disputes With No Paper Trail

A clinician thinks they were shorted. The owner thinks the check was right. Without a record of which visits counted and which rate applied, the disagreement comes down to memory. Most owners end up paying the difference just to keep the peace, whether or not it was owed.

Slow Payers Nobody Is Watching

Workers’ comp claims, auto and personal injury cases, and Medicaid can take months to pay. When the books only get looked at once a quarter, nobody notices that a payer has fallen behind or that takebacks are shrinking deposits. The first sign is usually cash running tight the week before payroll.

What Changes

Payday stops being a weekend project. Productivity reports go in, the calculations come back checked, and clinicians are paid correctly and on time every period. When someone asks how their check was figured, the answer is already written down. The owner gets evenings back, and the office manager can go back to keeping the schedule full.

Each month you know what was actually collected, not just what the billing system reports. Gaps get caught within weeks instead of surfacing at year end. Payroll runs in every state where you have staff. When tax season comes, the books are already in order, and our enrolled agents can prepare the practice and owner returns and set quarterly estimates without a scramble.

Clinicians Who Trust Their Pay

When pay is right every period and the math is easy to follow, there is much less to argue about. That matters in a field where clinicians have plenty of options and turnover is expensive. Marcella Nichols, our President, spent seven years in recruiting and HR before joining the firm. She knows how much an accurate, predictable paycheck has to do with keeping good people.

Numbers You Can Plan Around

With collections tied to actual deposits and pay calculated the same way every time, you can see how long each payer takes to pay and what each clinician’s pay costs the practice. You can tell whether the practice can support another hire or a second location. Decisions get made from real numbers instead of a rough sense of how the month went.

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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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