Bookkeeping and Tax for Philadelphia Medical Practices
Bookkeeping, payroll, and tax for Philadelphia physicians and practice owners, including city wage tax withholding and city business tax filings.
Bookkeeping and Tax for Philadelphia Practices
Philadelphia is a doctor’s town. Penn, Jefferson, Temple, and CHOP train thousands of residents and fellows, and a good share of them stay. Some build long careers inside the health systems. Others eventually leave to open practices in Center City, the Northeast, or out on the Main Line. Either way, the money side tends to get more complicated than people expect. Part of that is because Philadelphia taxes wages and business activity on its own terms, on top of what Pennsylvania and the IRS already collect.
Baker’s Bookkeeping & Tax Services has been doing tax and bookkeeping work since 1995, starting in Lenexa, Kansas. Our remote division was built for independent practices and the physicians who run them. Our CIO, Marc Eastin, is a practicing neurosurgeon who also owns a business, so we know what it’s like to finish a long day of patient care and still have payroll to approve. We provide medical practice bookkeeping and tax services to Philadelphia practices entirely online, with enrolled agents who take the time to learn how your practice actually runs.
Books That Match the Bank
Books That Match the Bank
Your books are closed every month with a one-page summary you can read in a few minutes. If you bill insurance, we compare what your billing system says was collected against what actually reached the bank. Gaps there are common and easy to miss. If the books are behind, we bring them current first.
Payroll With the City Wage Tax
Payroll With the City Wage Tax
Philadelphia’s wage tax applies to people who live in the city and people who commute in, at different rates. We run staff and provider payroll through Gusto with the right city, state, and federal withholding. Offices in the suburbs bring their own local earned income tax, and we handle that as well.
Federal, State, and City Returns
Federal, State, and City Returns
Federal and Pennsylvania returns for the practice and its owner, plus the city filings that apply to you, such as the Business Income and Receipts Tax and the Net Profits Tax. Enrolled agents prepare the returns and answer IRS, state, or city notices so you don’t have to.
Planning Before Year End
Planning Before Year End
Each added layer of tax raises the stakes on decisions like an S-corp election, how much salary the owner takes, retirement contributions, and when to buy equipment. We build a yearly plan around those choices and check in on it so the spring tax bill isn’t a surprise.
Philadelphia Practices We Work With
The big academic health systems anchor medicine in Philadelphia, but they aren’t the whole picture. Around them are independent practices of every size. Primary care offices in the Northeast, surgical groups along the Main Line, therapy practices in Chestnut Hill and Manayunk, aesthetic clinics near Rittenhouse Square. Most of them are run by people who are very good at patient care and never planned to become accountants.
Pennsylvania ranks among the top five states for concierge medicine, and the Philadelphia area has plenty of physicians who have made that move. Many trained or worked at a hospital here before deciding they wanted smaller patient panels and more time with each person. We do a lot of concierge and direct care bookkeeping for doctors in exactly that spot, running a business for the first time.
Concierge and Direct Primary Care
Concierge and Direct Primary Care
Membership revenue, retail products, and a new entity to keep track of. We set up the structure, books, payroll, and software before you see your first patient, then keep everything current once the practice is up and running.
Employed Physicians With Side Income
Employed Physicians With Side Income
Plenty of hospital-employed physicians here earn extra through expert witness work, locums, consulting, or medical directorships. Our side-income package for employed physicians covers the bookkeeping, quarterly estimates, and returns. In Philadelphia, that side income can also bring city filings many doctors don’t know they owe.
Behavioral Health Groups
Behavioral Health Groups
Therapy, psychology, and psychiatry groups that pay clinicians per session. We calculate each clinician’s pay every pay run based on the agreements you already have, then run payroll. Our president, Marcella Nichols, holds a master’s in clinical psychology and understands how these practices work.
Med Spas and Aesthetic Clinics
Med Spas and Aesthetic Clinics
Prepaid packages and memberships are money for treatments you haven’t delivered yet. We track them so revenue isn’t overstated, show your profit per treatment after product cost and commissions, and file sales tax on the skincare you sell.
Common Questions About This Area
You're based in Kansas. Why would a Philadelphia practice work with you?
Almost all of the work happens online. We keep books in QuickBooks Online, run payroll through Gusto, and meet by video when it helps. The firm has clients in nearly every state, and our remote division was built specifically for medical practices and the people who own them.
Do you handle Philadelphia's city taxes?
Yes. We withhold the city wage tax through payroll and prepare the Business Income and Receipts Tax and Net Profits Tax filings when they apply, along with your Pennsylvania and federal returns. If the city's Department of Revenue sends a notice, we deal with it.
I'm leaving a hospital job to open a concierge practice. When should I reach out?
Ideally before you sign a lease or give notice. Picking the right structure and setting up books, payroll, and software before opening saves a lot of cleanup later. New practice setup runs $500 to $5,000 one time, depending on what you need.
What does monthly bookkeeping cost?
Monthly bookkeeping runs $500 to $1,500 a month depending on the size of the practice. If your books are behind when we start, catch-up work is billed at 75% of the monthly fee for each month that needs to be brought current.
I'm employed by a health system but do expert witness work on the side. Can you help with that?
Yes. Our side-income package covers bookkeeping, quarterly estimates, and tax returns for doctors with 1099 or business income outside their main job. It runs $3,000 to $4,800 a year. Our CIO is a practicing neurosurgeon, so we know this situation well.
A Family-Run Firm Since 1995
Let's Talk About
Your Practice
Tell us about your practice and where you could use some help.
Other Areas We Serve
