Bookkeeping and Tax for San Diego Medical Practices
Bookkeeping, payroll, and tax for independent San Diego medical practices, med spas, and concierge and integrative clinics.
Bookkeeping and Tax for San Diego Medical Practices
Baker’s Bookkeeping & Tax Services has handled tax, bookkeeping, and payroll since 1995. The firm started in Lenexa, Kansas, and now works remotely with clients in nearly every state. Our remote division focuses on independent medical and healthcare practices, and San Diego has a lot of them.
We provide medical practice bookkeeping and tax services for San Diego physicians, med spa owners, and clinicians who run their own practices. Working here comes with a California layer. Payroll rules are stricter than in most states, sales tax applies to the skincare and supplements many practices sell, and the state income tax makes planning matter more for owners who earn well. We keep everything in QuickBooks Online and Gusto, and an enrolled agent handles your returns and any letters from the IRS or the Franchise Tax Board.
Monthly Bookkeeping
Monthly Bookkeeping
Books closed every month with a one-page summary you can read in a few minutes. For practices that bill insurance, we check that what your billing system reports as collected actually reached the bank. If your books are behind, we bring them current first.
California Payroll
California Payroll
Staff and provider payroll through Gusto. California has daily overtime, meal and rest break rules, and its own payroll filings with the EDD. We make sure front-desk staff, nurses, injectors, and providers are paid correctly, including providers who live or work in another state.
Practices With More Than One Entity
Practices With More Than One Entity
California is strict about who can own a medical practice. Many San Diego med spas run as a physician-owned medical corporation alongside a separate management company, and some physicians also own their building. Our multi-entity bookkeeping keeps each set of books separate and the transactions between them clean.
Tax Planning for High Earners
Tax Planning for High Earners
Practice owners in San Diego pay federal tax plus the highest top state income tax rate in the country. Each year we review your entity structure, owner salary, retirement contributions, and the timing of equipment purchases to lower the total bill. The goal is to plan for next year, not just file for last year.
San Diego Practices We Work With
San Diego patients spend money on their health and appearance, and the local practices reflect that. Aesthetic clinics fill storefronts in La Jolla, Del Mar, and UTC. Concierge and integrative practices are spread from Carmel Valley up to Encinitas. Physician and specialty offices cluster around Hillcrest and Kearny Mesa, close to the hospitals.
Many of these owners trained or worked at UC San Diego Health, Scripps, Sharp, or Kaiser before going out on their own. They know medicine well. Running payroll, tracking memberships, and dealing with California tax is newer territory. Our CIO, Marc Eastin, is a practicing neurosurgeon who also owns a business, so we understand what it is like to see patients all day and still be responsible for the books.
Med Spas and Aesthetic Clinics
Med Spas and Aesthetic Clinics
Injectables, lasers, body contouring, and skincare retail. We show profit per treatment after product cost and provider commissions, and we track prepaid packages so revenue isn’t counted before the service is delivered. Sales tax on retail products gets filed with the state on time.
Concierge and Integrative Medicine
Concierge and Integrative Medicine
Concierge physicians, direct primary care, and functional, hormone, weight-loss, and IV clinics. Revenue comes mostly from memberships, and many of these practices sell supplements too. Our work with direct care and integrative medicine practices often starts before opening day, with the structure, books, and payroll set up correctly from the beginning.
Physician and Surgical Practices
Physician and Surgical Practices
Dermatology, plastic surgery, orthopedics, OB/GYN, primary care, and other independent groups. We match insurance collections to bank deposits, calculate partner pay from the compensation agreements you already have, and keep the practice and building entities on separate books.
Doctors With Side Income
Doctors With Side Income
With so many life sciences companies around Torrey Pines and Sorrento Valley, many employed physicians here earn extra income consulting, serving on advisory boards, working as medical directors, or picking up locums shifts. We handle the bookkeeping, quarterly estimates, and returns that come with that 1099 income.
Common Questions About This Area
Do you work with practices throughout San Diego?
Yes. We work with practices in La Jolla, Del Mar, Carmel Valley, Hillcrest, Kearny Mesa, Mission Valley, and across North County and the South Bay. All of our work is remote. Our team is on Central time, two hours ahead of you, so questions you send in the morning are usually answered the same day.
Your office is in Kansas. Can you handle California requirements?
Yes. We have clients in nearly every state, and California has more rules than most. We run payroll through Gusto with California's overtime and break rules in mind, file sales tax with the CDTFA, and prepare your state returns. Enrolled agents respond to any notices from the Franchise Tax Board or the IRS.
What does monthly bookkeeping cost?
Most practices pay between $500 and $1,500 a month, depending on transaction volume and how many entities you have. If your books are behind when we start, catch-up work is billed at 75% of the monthly fee for each month we bring current. We give you an exact quote after we look at your situation.
I'm leaving a health system to open a concierge or integrative practice. When should I reach out?
Before you open, if you can. We help choose the business structure, set up QuickBooks Online and Gusto, and get payroll ready so your first month runs smoothly. It is much easier to start correctly than to fix things after patients are already paying memberships.
Can you help us hire staff?
Yes. Hiring nurses, aestheticians, and front-desk staff in San Diego is competitive. Our President, Marcella Nichols, spent seven years in recruiting and HR at a large Southern California software company. We write job descriptions, benchmark pay against the local market, prepare offer letters and onboarding paperwork, and build your employee handbook.
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