Skip to content Skip to footer
Schedule a Call
Schedule a Call
Close

  ● Healthcare Bookkeeping

Outsourced Bookkeeping for Medical Practices

Clean books, provider-level financials, and tax-ready records without carrying an in-house accounting team. CountSure supports independent practices, group practices, and multi-site healthcare organizations across the United States.

Schedule a Consultation
See What We Handle
✓ CPA-Led Engagement Oversight
✓ US GAAP & IRS Compliant
✓ Signed BAA & Strict Data Security
✓ QuickBooks, Xero & PM/EHR Ready
✓ CPA-Led Engagement Oversight
✓ US GAAP & IRS Compliant
✓ Signed BAA & Strict Data Security
✓ QuickBooks, Xero & PM/EHR Ready

  ● Healthcare Bookkeeping

What Outsourced Bookkeeping for Medical Practices Covers?

Outsourced bookkeeping for medical practices is the ongoing recording, reconciliation, and reporting of a practice’s financial activity by an external accounting team. It covers insurance remittances, patient payments, payroll, vendor spend, and the monthly close that turns all of it into financial statements you can act on. CountSure delivers it as a managed service built on the same outsourced bookkeeping services and monthly financial statements and reporting we provide across every industry rebuilt around how healthcare revenue actually arrives.

It is not medical billing. Your biller decides what gets claimed. Your books decide what the practice actually earned, kept, and owes.

  • The result
  • Books closed every month, not reconstructed in a panic at tax time
  • Revenue reported net of contractual adjustments, so your margins are real
  • Records organised the way a tax preparer actually needs to receive them

Medical Billing vs.Bookkeeping: Where One Ends and the Other Begins

Almost every practice we speak to has a biller. Very few have anyone reconciling what the biller produced against what the bank received. That gap is where profitability quietly disappears and it is the gap our accounts receivable and payable management and QuickBooks accounting support are designed to close.
Medical Billing RCM
Bookkeeping & Accounting
Core question
Did we get paid for the care we delivered?
What did the practice actually earn and keep?
Works inside
Practice management and EHR systems
The general ledger - QuickBooks, Xero
Primary output
Clean claims, appeals, aged AR by payer
Financial statements, tax-ready records
Measures success by
Collection rate and days in AR
Margin, cash position, cost per visit
When it's weak
Claims are denied, aged, or never worked
You are profitable on paper and short on cash
  • The handoff between them is the weak point. Billing reports what was posted; the bank reports what was deposited. When nobody ties the two together, months pass before anyone notices a payer has been underpaying a contracted rate.

Medical Practice

These are structural problems, not sloppiness. Healthcare revenue behaves differently from almost every other industry, and generic bookkeeping breaks against it.

Payer deposits arrive net, not gross.

You bill a charge; the payer pays a contracted rate; the difference is a contractual adjustment. Book the deposit as revenue and you understate gross production, losing all visibility into how much each payer discounts.

One deposit, dozens of patients.

A single ACH from a commercial payer can cover forty encounters across three providers. Without the remittance advice matched against it, the deposit lands in the ledger as one undifferentiated line.

Refunds and credit balances inflate revenue.

Overpayments, coordination-of-benefits corrections, and patient credit balances are liabilities, not income. Sitting in a revenue account, they report money the practice will have to give back.

Provider compensation gets tangled with payroll.

Owner draws, partner distributions, productivity bonuses, and W-2 salary often flow through the same accounts. The practice then cannot tell what any individual provider contributes to the bottom line.

Supply and equipment spend goes uncategorised.

Medical supplies, pharmaceuticals, lab fees, and capital equipment carry different tax treatments. Lumped into one expense line, they cost the practice deductions it was entitled to.

Recognise any of these in your own books? A CountSure specialist will review your current setup and tell you plainly what it would take to fix.

Schedule a Consultation

What We Handle for Your Practice ?

Every item below is delivered by accountants who understand healthcare revenue not generalists learning your business on your time.

Monthly Close with Provider and Location P&L

We close monthly and report at the level you manage the business per provider, per location, per service line and not one consolidated statement.

Deposit-to-Remittance Reconciliation

We match every payer deposit against its remittance advice, so posted payments, contractual adjustments, and write-offs reconcile to the bank rather than being assumed.

Accounts Payable & Vendor Management

We process supply, pharmaceutical, lab, and service-vendor invoices, track payment schedules, and code spend to the categories your tax position depends on.

Tax-Ready Books & CPA Coordination

We prepare the books specifically for filing and coordinate with your tax preparer, or handle the return through CountSure’s own US tax team.

Payroll, Provider Compensation & 1099 Support

We separate W-2 payroll from owner draws, distributions, and productivity compensation, and maintain contractor records for locum tenens providers.

Payer and Patient Payment Posting Review

We break bundled payer deposits into component payments, separating patient responsibility, refunds, and credit balances from genuine revenue.

Catch-Up and Cleanup Bookkeeping

If the books are months behind, we reconcile prior periods, correct miscoded transactions, and set a clean baseline before ongoing work begins.

Equipment & Leasehold Depreciation Schedules

We maintain fixed asset registers and depreciation schedules for clinical equipment, imaging, and build-outs, aligned with IRS guidance.

Practices that need staffing rather than a managed service can instead hire Countsure.

Practice Types We Support

The reporting a two-provider clinic needs is not what a six-site group needs. We scope to the structure you operate.

  • Solo and independent physician practices
  • Multi-provider group practices
  • Dental and orthodontic practices
  • Urgent care and walk-in clinics
  • Physical therapy, chiropractic, and rehabilitation clinics
  • Behavioural and mental health providers
  • Med spas and elective or cash-pay practices
  • Multi-site groups, MSOs, and management companies

How We Handle PHI and HIPAA ?

Bookkeeping does not require patient charts. It can touch remittance and payment data carrying protected health information, and that changes the compliance posture of the engagement.
Under HHS guidance, an outside firm performing accounting services involving the use or disclosure of PHI on behalf of a covered entity is a business associate, requiring a signed Business Associate Agreement before data is shared.

How we work in practice?

  • We request summary and de-identified financial data wherever the work allows it
  • We sign a BAA and an NDA before system access is granted
  • Access is role-based and limited to the minimum necessary for the task
  • No PHI moves through ordinary email; transfers use controlled channels only
PHI and HIPAA compliant bookkeeping for medical practices

Systems We Work In

You do not need to change platforms. We operate inside your existing accounting stack and take financial data from your PM or EHR system in whatever format it exports.

Practice management and EHR

We work from reports, remittance files, and payment registers exported from your PM or EHR system, so no clinical system migration is required.

Accounting and operations

  • QuickBooks Online and QuickBooks Desktop
  • Xero
  • Bill.com, Expensify, and comparable AP and expense tools
  • Gusto, ADP, and comparable payroll platforms

How Onboarding Works?

A structured start, built to avoid disrupting a practice that is already running at capacity.

  • Discovery Call

    A short consultation covering practice structure, payer mix, current accounting setup, and the reporting you need each month.

  • Scope and Proposal

    A written scope naming deliverables, reporting cadence, and fee - sized to your transaction volume, not a fixed package.

  • Secure Onboarding

    BAA, NDA, and role-based access are established before data moves. We connect to your accounting platform and agree what you will send from your PM or EHR system.

  • Clean-up, Then Cadence

    Where the books are behind, we clear the backlog first. From there: a monthly close, provider-level reporting, and a named point of contact.

Frequently Asked Questions

Medical billing gets claims paid; bookkeeping records what those payments did to the practice’s finances. Billing lives in your practice management system and is measured on collection rate and days in AR. Bookkeeping lives in the general ledger and produces financial statements and tax records. Most practices have the first and lack the second.

In most engagements, no. The work can generally be done from bank data, remittance summaries, and payment registers rather than clinical records. Where PHI is genuinely required, we sign a Business Associate Agreement first and limit access to the minimum necessary.

Yes, and it is the most common arrangement. We sit between them reconciling what your biller posted against what the bank received, then delivering tax-ready books to your CPA. CountSure can also handle the return if you prefer one provider.

Yes. Catch-up work is a common starting point. We assess how far behind the records are, give you a timeline to bring them current, then transition into ongoing monthly close.
Yes. We structure the chart of accounts so revenue and expenses are coded to the provider, location, or service line that generated them giving you per-provider and per-site profit and loss alongside consolidated statements.
No. We work in QuickBooks Online, QuickBooks Desktop, and Xero, and take data from your existing PM or EHR system in whatever format it exports. No clinical system migration is involved.
Pricing depends on transaction volume, number of providers and locations, payer complexity, and whether catch-up work is needed. We provide a written proposal after the consultation rather than quoting a package price up front.

Get Started

Keep Your Medical Practice Financials
Clean & Tax-Ready

Talk to our bookkeeping experts and get reliable financial records without the cost of an in-house accounting team.

  • No obligation consultation
  • Response within 12 hours
  • 100% confidential
  • IRS-compliant, audit-ready reports

    Go To Top Schedule Icon Schedule a Free Consultation