How to Set Up Medical Billing in a New York Practice

Starting a medical practice in New York is exciting, but one of the most important—and complex—parts of running it is setting up medical billing. Without a streamlined billing process, practices risk delayed payments, compliance issues, and frustrated patients. Whether you’re opening a solo office or managing a multi-provider clinic, here’s a step-by-step guide to getting your billing operations in place.

1. Establish the Legal & Compliance Foundation

Before you can bill insurers or patients, you need to ensure your practice is properly registered and compliant:

• Business Registration: Register your business entity (professional corporation, LLC, etc.) in New York; ensure provider/facility licensure.
• Provider Credentialing: Obtain EIN (tax ID), NPIs, and make sure all provider credentials (medical license, board certification, malpractice insurance) are current.
• CAQH Profile: Keep your Council for Affordable Quality Healthcare profile accurate and updated, it’s essential for insurance credentialing.
• For labs: ensure CLIA certification; for any facility: ensure required safety / regulatory certifications.
• HIPAA Compliance: Set up secure processes for handling patient health information and ensure your EMR or billing system is HIPAA-compliant.

2. Complete Insurance Credentialing

To get reimbursed, you must be enrolled with the payers you plan to bill claims to. In New York, this often includes Medicare, Medicaid, and a mix of commercial insurers.

• Medicare: Apply through PECOS (Provider Enrollment, Chain, and Ownership System).
• Medicaid: Enroll via eMedNY, the state’s Medicaid billing platform.
• Commercial Payers: Apply to join networks such as Empire BlueCross BlueShield, Aetna, Cigna, and UnitedHealthcare. Credentialing usually takes 60–120 days.
• Workers’ Compensation & Third-Party Liability Insurance: If you’ll treat patients with work or accident-related injuries, register with the New York Workers’ Compensation Board and the Department of Financial Services.

3. Choose Your Billing Setup

There are two main ways to manage billing:

• In-House Billing: You hire staff and manage claims directly through your EMR or billing software. This gives you control but requires training, staff costs, and ongoing oversight.
• Outsourced Billing: You contract with a billing service that handles claims, denials, and collections on your behalf. This can reduce administrative burden but typically involves a percentage-based fee.

4. Implement Systems & Processes

Once credentialed, put the right systems in place to keep billing accurate and efficient:

• EMR & Practice Management Software: Select a practice management system or EMR that combines scheduling, clinical documentation (charting), and billing functions in one platform. Make sure it connects directly with a clearinghouse so you can submit electronic claims, track rejections, and receive remittance information efficiently.
• Claim Scrubbing: Use tools, such as a clearinghouse, to check claims for errors before submission. When a claim is rejected by the clearinghouse, it is not forwarded to the insurance payer. The clearinghouse will return error codes explaining why the claim failed. These errors must be corrected, and the claim resubmitted, before the payer can receive and process it.
• Payment Posting: Enter all payments and adjustments from insurers and patients into your billing system. Match each payment against the original claim and reconcile with the Explanation of Benefits (EOB) or Electronic Remittance Advice (ERA) to ensure accuracy.
• Denial Management: Create a structured process for handling denied or rejected claims. This should include reviewing denial codes, identifying the root cause (e.g., missing information, coding error, lack of prior authorization), correcting errors, and resubmitting or appealing the claim within the payer’s deadline. Tracking denial trends also helps prevent recurring issues.
• Patient Billing: clearly state financial responsibility, co-insurance/copay/deductible, payment plans; for self-pay/uninsured, issue good faith estimate when required.

5. Train Your Staff

Even with great systems, billing success depends on knowledgeable staff. Train front-desk and billing teams to:

• Verify insurance and benefits before appointments to confirm coverage and network status.
• Collect co-pays and outstanding balances at check-in when appropriate.
• Document services with correct CPT, HCPCS, and ICD-10 codes to ensure accurate claims.
• Explain financial policies clearly so patients understand their responsibility, payment options, and assistance programs.

6. Monitor and Optimize

Billing is not “set it and forget it.” To keep revenue healthy, practices should:

• Review denial and rejection trends to find and fix recurring issues.
• Track key metrics such as days in accounts receivable (A/R) to monitor cash flow.
• Stay current with coding and compliance updates (CPT, HCPCS, ICD-10, payer policies, and federal/state regulations).
• Analyze financial reports to forecast revenue, identify gaps, and adjust processes as needed.

Final Thoughts

Setting up medical billing in a New York practice takes careful planning, but the effort pays off in smooth cash flow and reduced compliance risks. From credentialing with insurers to choosing the right billing system, every step builds the foundation for a financially healthy practice. Whether you keep billing in-house or outsource, the key is to stay compliant, stay consistent, and continuously improve your processes.

OptiMantra makes it easy for New York practices to get started confidently and efficiently. Our fully integrated EMR and practice management platform includes end-to-end insurance workflows, and an optional revenue cycle management (RCM) solution to simplify billing even further. With OptiMantra, you can manage claims efficiently, maximize reimbursements, and keep your revenue cycle running smoothly, all in one system.

‍Ready to streamline billing and boost revenue in your New York practice?

Schedule a demo with OptiMantra today and see how our all-in-one EMR and practice management solution can help your practice thrive.

*This article is for informational purposes only. Always consult a qualified legal or compliance professional when setting up a medical practice and arranging billing systems.