Bookkeeping Services for Doctors: Fixed-Fee Plans for Medical Practices

Bookkeeping services for doctors at GATP start at less than $250 a month, a fraction of the $73,795 a year a full-time in-house bookkeeper costs once benefits are added. You get a CPA firm that records every insurance deposit, patient payment, payroll run and bill, then closes your books on a fixed schedule.

Most practices call us when the numbers stop making sense. Revenue looks strong, yet cash is tight, or the profit and loss does not match the billing system. Our bookkeeping sits inside the same team that handles medical practice accounting and tax. Your books, payroll and return run on one set of numbers.

What Our Bookkeeping Services for Doctors Include

Our bookkeeping services for doctors are monthly recordkeeping, reconciliation and reporting built around how your practice earns and spends money. The work covers payer and patient receipts, practice bills, payroll entries and a month-end close you can rely on.

Medical bookkeeping services differ from a general package on the revenue side. Payer deposits, contractual adjustments and patient balances each get their own accounts and their own checks. Here is what every engagement delivers:

Medical billing, coding and claim follow-up are not part of our scope. Your billing team or company produces the claims, and our medical bookkeeper records and reconciles what those claims turn into.

Even the Lite plan, from under $250 a month, includes setup and backlog work. The service runs on the same process as our outsourced bookkeeping for other industries, with healthcare accounts added. The month-end mechanics, from payer reconciliation to the chart of accounts, follow the steps in our guide to bookkeeping for doctors.

Who Our Medical Bookkeeping Services Are Built For

Our medical bookkeeping services are built for established physician-owned practices with staff, several payers and often more than one location. The work changes with how your practice is structured, so the plan does too.

Most practices we work with fall into one of three shapes:

Solo Physician Practices

A solo physician practice usually runs one operating account, one or two cards and a short list of payers. The bookkeeping is light, but the mistakes are personal. Practice and household spending share one card, and an S corporation salary never gets separated from distributions.

For a solo practice we focus on three things:

• One clean practice account, with personal spending moved out of the books.
• Owner pay and distributions posted to the right accounts every month.
• A contractor list kept current for Form 1099-NEC, which the IRS 1099-NEC instructions now require at $2,000 or more.

Most solo practices fit the Lite plan, with books closed monthly and replies within 96 hours. If you also want tax planning, Plus adds it twice a year. Either way, your first month starts with a clean split between practice and personal money, because every later report depends on it. You also get one person to ask, instead of a different answer from each tool you use.

Group Practices With 2 to 10 Providers

Bookkeeping services for medical practices of this size have to split revenue and cost by provider. Without that split, partners cannot see who produces what, and compensation formulas run on guesses.

For a group practice we add three recurring jobs:

• A class or location tag on every revenue and expense line.
• Payroll posted every cycle, with physician pay kept apart from staff wages.
• A receivables tie-out against your practice management aging report before each close.

Groups usually fit Plus, with weekly bookkeeping, payroll, bill payment and a quarterly session with a dedicated CFO. We close the month before your compensation report runs, so partners are paid on final numbers.

You also see each provider’s allowed amounts, direct costs and payroll side by side, which is the report most partner meetings argue about. If a new physician joins mid-year, the class is added before their first visit posts.

Multi-Location Practices and MSO Structures

A multi-location practice or a practice run through a management services organization keeps separate books for each entity. Each set closes on its own, then the group consolidates them.

The work our team handles at this size includes:

• Management fees between the practice and the management company, each backed by a calculation.
• Drug and supply purchases posted by location before each close.
• Intercompany balances that agree on both sides, then consolidated statements.

A multi-location rheumatology practice came to us with an unsupported management fee and unrecorded McKesson drug invoices at one clinic. Premium fits this shape: daily bookkeeping, a monthly CFO session and federal and state tax filing.

Each entity closes on the same calendar, so the consolidated report reaches you with every intercompany balance already agreed. When a new location opens, it gets its own books from the first deposit rather than a clean-up a year later.

How Much Do Bookkeeping Services for Doctors Cost?

Bookkeeping services for doctors at GATP start at less than $250 a month on a fixed fee, while a full-time in-house bookkeeper costs about $73,795 a year with benefits. The in-house figure starts with the BLS May 2025 wage data, a median of $50,670 for bookkeeping clerks.

Employers pay $11.51 in benefits for every $25.22 of wages in office and administrative roles, per the BLS employer cost survey for June 2026. That adds $23,125 to the salary and puts the loaded hourly cost at about $35.48. Our three fixed-fee plans compare like this:

Your fee depends on transaction volume, payer count, payroll size and the number of entities. To compare a quote against hiring, divide it by $35.48: a fee that buys 20 hours of in-house time is about $710 a month.

Should a Medical Practice Outsource Its Bookkeeping or Hire an In-House Bookkeeper?

Most solo and group practices should outsource their bookkeeping and keep one internal person in charge of approvals. An in-house hire makes sense when the work fills a full-time role and someone must sit with the front desk every day.

The trade-offs look like this:

Outsourcing moves the work, not the responsibility. You still approve payments and read the monthly report. The same split applies to outsourced accounting for medical practices, where review sits outside and approvals stay inside.

How Our Bookkeeping Engagement Works

Our bookkeeping engagement runs in five steps, from the first call to a steady monthly close. Each step exists to stop a specific problem that shows up later in the books:

1. Discovery call. One of our owners replies within one business day to book it. We learn your payers, entities, software and billing setup, so the plan fits the practice you actually run.
2. Proposal call. Within several days you get three priced options, plus a demo of the software we recommend. You choose the scope instead of guessing at it.
3. Books setup. We build a healthcare chart of accounts with payer classes and provider tags. Reports can only show what the accounts were built to hold.
4. Backlog catch-up. Missing months are rebuilt in order and reconciled to each statement. The monthly service then starts from a clean opening balance.
5. Monthly close. Deposits are matched, adjustments recorded and receivables tied to your aging report before the statements go out.

Every engagement is an annual contract with a 30-day notice period to cancel or change it, and plans start at less than $250 a month. As a virtual firm, we work with you by email, phone, Zoom and Google Meet, with Slack or WhatsApp on the higher plans.

How We Keep Patient Data Out of Your Books

Patient data stays out of your books because we post payer and date totals, not patient names, dates of service or diagnosis codes. Most bookkeeping needs no protected health information at all.

That matters for two reasons. The HHS business associate guidance, last reviewed on July 30, 2026, names a CPA firm whose accounting work involves access to patient information as a business associate. Under 45 CFR 164.502(e), your practice needs a signed agreement before that firm sees the data.

Second, Intuit’s QuickBooks Online help page says the product is not compliant with the HIPAA standards for privacy. So our posting rules are simple:

• Remittance detail stays in your practice management system, where access controls already exist.
• Only summarized deposits, adjustments and receivable balances reach the ledger.
• Patient names are stripped from refund records before they are entered.
• If your practice needs patient-level reports reviewed, a business associate agreement comes first.

What Practices Fix When They Move Their Books to GATP

Practices that move their books to GATP usually fix one of three problems. Revenue is booked at the wrong amount, receivables do not match billing, or several businesses share one account. Each case below comes from a published GATP engagement.

The pattern in every case was the same. The books looked tidy and the numbers were still wrong:

• Six-entity medical group: over $1.3M in revenue and $800K to $980K of receivables a month. Voided portal invoices still sat in QuickBooks as open receivables, so the receivables balance was overstated. Our healthcare accounts receivable reconciliation now runs mid-month and again before financials go out.
• Rheumatology group: revenue sat at gross charges with no insurance adjustments, and a stopped card feed hid a full month of expenses. Profit looked higher than it was until both were fixed.
• Physician-owned integrative practice: a clinic, a supplement store and a course business ran through one Square account. Deposits arrive net of fees and refunds, so revenue booked off sales reports never tied to the bank. The medical practice bookkeeping rebuild split the three revenue streams and recorded fees as their own lines.

How to Choose Bookkeeping Services for Your Medical Practice

Choosing bookkeeping services for your medical practice comes down to six questions you can put to any provider, us included. Each one prevents a mistake practices make with the wrong firm:

1. How do you reconcile payer deposits? This prevents revenue booked at gross charges.
2. Can I see a sample month-end report with provider-level results? This prevents a profit and loss that cannot show which physician or location makes money.
3. Do you need patient-level data? If yes, sign a business associate agreement first. This prevents a HIPAA gap with an outside vendor.
4. When do my financials arrive each month? This prevents decisions made on last quarter’s numbers.
5. Who prepares the tax return? A firm that keeps the books and files the return avoids a year-end handoff.
6. Who owns billing and coding? This prevents denied claims falling between two vendors.

The fifth question is where a CPA firm earns its fee. GATP has served businesses since 2012, and a CPA for doctors who already keeps your books starts the return from a closed, reconciled year.

Conclusion: Bookkeeping Services for Doctors That Close on Time

Bookkeeping services for doctors should deliver reconciled payer deposits, payroll and bills, plus a monthly report you can act on, for well under the $73,795 a year an in-house hire costs. GATP’s fixed-fee plans start at less than $250 a month and scale from monthly to daily bookkeeping as your practice grows.

Get a fixed-fee quote for your practice books. Tell us your payers, entities and billing setup on a 30-minute call. We review how your deposits, adjustments and receivables post today, and you get three priced options for our healthcare accounting services within several days. Book a 30-minute call.

Frequently Asked Questions About Our Bookkeeping Services for Doctors

How Quickly Can You Start on Our Practice’s Books?

One of our owners replies within one business day to book a discovery call. Within several days of that call you get three priced options to choose from. Once you pick one, we set up the books and start on any backlog before the first monthly close.

Do You Work With Our Billing Company?

Yes. Your billing company submits claims and works denials, and we record and reconcile what those claims produce. We ask billing for remittance totals and the aging report each month. A payer gap we find goes back to them, because a denial is a billing task, not a bookkeeping entry.

What Software Do You Use?

We work in your existing cloud accounting ledger and connect your practice management system’s totals to it. Depending on the plan, our stack adds Dext for receipts, a SaaSant importer, Bill.com for bill payment and Fathom for reporting. Patient-level detail stays in your billing system.

What If Our Practice Books Are Months Behind?

Every plan includes updating your backlog. We rebuild the missing months in order, reconciling each bank and card account to its statement and recording contractual adjustments as we go. Your monthly service then starts from a clean opening balance.

Do You File the Practice’s Tax Return?

Federal and state tax filing is included in the Premium plan. Plus includes tax planning twice a year, and Premium includes it every quarter. On Lite, our tax team prepares the return as a separate engagement, starting from the closed, reconciled year we already keep.

Is There a Long-Term Contract?

Every engagement is an annual subscription contract with a 30-day notice period to cancel or change it. If your needs do not fit one of the three plans, we build a tailored option during the discovery call. Plans start at less than $250 a month, and prices are set before work starts, so there are no hourly surprises.

Can You Work With Our Office Manager?

Yes, and the best setups depend on it. Your office manager approves bills, answers questions on deposits and keeps front desk posting clean. We do the recording, reconciliation and reporting, and a shared monthly checklist keeps both sides on the same close date.