Bookkeeping and Tax for San Francisco Medical and Therapy Practices
Bookkeeping, payroll, and tax for San Francisco concierge, integrative, and therapy practices. Remote service from a family firm doing this work since 1995.
Cash-Pay Medicine in San Francisco
San Francisco patients will pay out of pocket for more time with a doctor. That has made the city one of the strongest markets in the country for concierge medicine, functional and integrative care, and hormone, weight-loss, and longevity clinics. Many of these practices were opened by physicians who left a hospital system or a large group because they wanted to practice differently. They know medicine well. Most have never run payroll or read a balance sheet for a business they own.
Baker’s Bookkeeping & Tax Services has done tax and bookkeeping work since 1995, and our remote division now provides medical practice bookkeeping and tax services to independent practices across the country. We’re based in Lenexa, Kansas, not San Francisco, and we won’t pretend otherwise. What we offer is a narrow focus on practices like yours and a team that understands the doctor’s side of things. Our Chief Information Officer, Marc Eastin, is a practicing neurosurgeon who also owns a business.
Set Up Before You Open
Set Up Before You Open
Leaving employment means building everything an employer used to handle for you. We set up the business structure, QuickBooks Online, Gusto payroll, and a chart of accounts that fits a membership practice. California generally requires medical practices to be owned by physicians through a professional medical corporation, so we plan the structure with that in mind and work alongside your attorney.
Membership Revenue Recorded Correctly
Membership Revenue Recorded Correctly
An annual membership paid in January covers care you’ll provide through December. We record it that way so your monthly numbers show what you actually earned. It’s one of the first things we check when working with concierge and integrative medicine practices, because getting it wrong makes a young practice look healthier than it really is.
Supplements and Retail Sales
Supplements and Retail Sales
Functional and integrative practices often sell supplements or skincare out of the office or through an online store. Those sales can carry California sales tax. We track them separately from medical services and file returns with the CDTFA on time, along with any other states you ship to.
Planning Around California Taxes
Planning Around California Taxes
California’s top income tax rate is 13.3 percent, and the state doesn’t follow federal rules on everything. Its limit on writing off equipment purchases is a small fraction of the federal limit, for example. Our enrolled agents build a yearly plan covering entity structure, owner salary, retirement contributions, and the state’s pass-through entity tax election so you keep more of what the practice earns.
Therapy and Psychology Groups in San Francisco
San Francisco has one of the largest communities of therapists, counselors, and psychologists in the country. Many work in solo private practice. A growing number have built group practices with associates, licensed clinicians, and a small front office. Once a group reaches three or four clinicians, the owner usually spends far more time on payroll and paperwork than they expected when they started.
Our President, Marcella Nichols, holds a master’s degree in clinical psychology and spent seven years in recruiting and HR before joining the firm. She understands how clinicians think about their work and how they expect to be paid. For most group owners, paying clinicians correctly every pay run is the hardest part of running the practice, so that is where we put the most care.
Session-Based Clinician Pay
Session-Based Clinician Pay
Per-session rates, different rates by service type, late cancellations, and no-shows all add up quickly. We take the compensation agreements you already have and apply them through clinician pay calculations that are checked before anyone gets paid. We don’t design pay plans or advise on them. We make sure the plan you have is followed exactly.
California and San Francisco Payroll
California and San Francisco Payroll
California requires registered associates such as AMFTs and ACSWs to be paid as employees, not contractors. San Francisco adds its own minimum wage, paid sick leave rules, and health care spending requirements once you reach 20 employees. We run payroll in Gusto and keep track of these rules as your practice grows.
Insurance and Private Pay
Insurance and Private Pay
Many San Francisco therapists are out of network and give clients superbills. Others take insurance for some clients and private pay for the rest. Each month we compare what your practice management system says was collected against what actually reached the bank, so missing payments get noticed in weeks instead of at tax time.
Hiring Clinicians in an Expensive City
Hiring Clinicians in an Expensive City
Finding clinicians who can afford to live and work in San Francisco is hard. We write job descriptions, benchmark pay against the local market, prepare offer letters and onboarding paperwork, and build an employee handbook. This work comes straight from Marcella’s years leading a recruiting team in California.
Common Questions About This Area
You're based in Kansas. How does that work for a San Francisco practice?
Everything runs remotely through QuickBooks Online, Gusto, secure document sharing, and video calls. We're two hours ahead of you, so your morning is our midday. The firm already has clients in nearly every state, and our remote division was built specifically for practices outside the Kansas City area.
Do you handle California tax filings?
Yes. Our enrolled agents prepare federal and California returns for the practice and its owner, set quarterly estimates for both, and respond to IRS and Franchise Tax Board notices. We're a bookkeeping and tax practice, not a CPA firm.
What does monthly bookkeeping cost?
Between $500 and $1,500 per month, depending on transaction volume and complexity. If your books are behind when we start, catch-up work is billed at 75 percent of the monthly fee for each month we need to bring current. Payroll starts at $150 per month.
I'm leaving a hospital job to open a concierge practice. When should I call?
Before you sign a lease if you can. New practice setup covers business structure, books, payroll, and software so everything works on the day you see your first member. It runs $500 to $5,000 one time, depending on what you need.
Will you tell us how to pay our therapists?
No. Clinician compensation is subject to compliance rules, and how you structure it is a decision for you and your attorney. We apply the agreements you already have, calculate pay each pay run, and run the resulting payroll accurately and on time.
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