Bookkeeping and Tax for New York City Medical Practices
Bookkeeping, payroll, and tax for New York med spas, concierge practices, specialty groups, and therapy practices. Remote service from a firm founded in 1995.
Bookkeeping and Tax for New York Practices
New York City has more med spas than any other market in the country, along with the largest concentration of concierge and direct primary care physicians, most of them in Manhattan and Brooklyn. Add the independent specialists and the therapy and psychology groups spread across the five boroughs, and the city has one of the densest collections of privately owned practices anywhere. Our work with med spas and aesthetic clinics and other independent practices starts from a simple fact. The numbers in a New York practice have more layers than they do almost anywhere else.
Owners here deal with state income tax, a separate city tax, high rent, and staff who commute in from three states. Baker’s Bookkeeping & Tax Services has prepared tax returns since 1995 from our home base in Lenexa, Kansas, and our remote division now serves practice owners nationwide. Your books, payroll, and returns are handled by a small team of enrolled agents who learn how your practice runs, working in QuickBooks Online and Gusto.
Monthly Bookkeeping
Monthly Bookkeeping
Your books are closed every month with a one-page summary of where the practice stands. If you bill insurance, we compare what your billing system says was collected with what actually reached the bank, a gap that shows up often in busy practices. Books that are months behind get brought current first.
Tax Returns and Planning
Tax Returns and Planning
New York City does not recognize the federal S corporation election, so an S corp practice still owes the city’s General Corporation Tax, and a PLLC taxed as a partnership may owe the Unincorporated Business Tax. Our tax services for physicians plan structure, owner pay, and retirement contributions with those city taxes in view. Enrolled agents handle notices from the IRS, the state, and the city.
Payroll Across State Lines
Payroll Across State Lines
A Midtown practice might have a nurse from Hoboken, a physician from Greenwich, and a front desk coordinator from the Bronx. We run staff and provider payroll through Gusto in any state, with New York Paid Family Leave, disability withholding, and the MTA payroll tax handled where they apply.
Hiring and HR Support
Hiring and HR Support
Good medical assistants and front desk staff are hard to find and harder to keep in this city. New York City requires most employers to post salary ranges and has its own paid sick leave law. Marcella spent seven years in recruiting and HR, and she helps with job descriptions, pay benchmarks, offer letters, onboarding paperwork, and an employee handbook.
New York Practices We Work With
Many of the practice owners we talk to in New York spent years inside a hospital system or a large group before opening their own office. They know medicine well. The business side, with its membership revenue, provider pay, payroll taxes, and city filings, is newer territory, and it tends to land on the owner’s evenings and weekends.
Our team was built with that in mind. Marc Eastin, our Chief Information Officer, is a practicing neurosurgeon who also owns a business, so he knows what it is like to be the client. Marcella Nichols, our President, holds a master’s in clinical psychology and has a real feel for how behavioral health practices pay their clinicians. Between them they understand how doctors and clinicians actually work.
Med Spas and Aesthetic Clinics
Med Spas and Aesthetic Clinics
We track profit per treatment after product cost and provider commissions, and we record prepaid packages and memberships so revenue isn’t overstated. New York’s corporate practice of medicine rules lead many med spas to operate as a physician-owned medical entity plus a management company, and our multi-entity bookkeeping keeps both sets of books clean and separate. Sales tax on retail skincare gets filed on time too.
Concierge and Direct Primary Care
Concierge and Direct Primary Care
Manhattan and Brooklyn have more concierge and direct primary care doctors than anywhere else in the country. Revenue arrives as monthly or annual memberships, and we record it so your reports reflect the care you’ve actually delivered. If you’re still planning your practice, we can set up the entity, books, payroll, and software before you open.
Independent Specialty Practices
Independent Specialty Practices
Dermatology, orthopedics, cardiology, GI, pain management, and the many other specialists running private offices across the city. We check insurance collections against bank deposits, calculate partner and provider pay each month from the compensation agreements you already have, and keep separate books if the practice owns its building.
Therapy and Psychology Groups
Therapy and Psychology Groups
Group practices with three or more clinicians, many of them partly or fully out of network. Clinician pay is calculated every pay run from your existing session-based agreements, so your therapists are paid correctly and on time. We don’t design compensation plans. We make sure the ones you have are applied the same way every time.
Common Questions About This Area
You're based in Kansas. Why would a New York practice work with you?
Nearly all bookkeeping and tax work happens online now, and we already have clients in almost every state. What matters more than our zip code is that we focus on independent medical and healthcare practices and know New York's state and city rules. Your work is handled by a small team of enrolled agents who learn your practice, not a call center.
Do you understand New York City's business taxes?
Yes. The city does not recognize the federal S corporation election, so S corp practices still owe the General Corporation Tax. Partnerships and PLLCs may owe the Unincorporated Business Tax. We factor these in when we prepare returns and when we plan owner pay and structure for the coming year.
What does monthly bookkeeping cost?
Monthly bookkeeping runs $500 to $1,500 per month depending on transaction volume and how complex the practice is. If your books are behind when we start, catch-up work is billed at 75% of the monthly fee for each month we need to bring current. We give you an exact quote after we look at your practice.
Can you run payroll for staff who live in New Jersey or Connecticut?
Yes. Many New York practices have providers and staff commuting from New Jersey, Connecticut, Long Island, and Westchester. We run payroll through Gusto in any state and keep the withholding right for each person based on where they live and work.
We're opening a concierge practice in Brooklyn. When should we bring you in?
Ideally a few months before you open. We can set up the business structure, books, payroll, and software before your first patient, so membership fees are recorded correctly from day one and you aren't fixing setup mistakes during your first tax season.
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