Primary Care Billing Challenges: Common Issues and Solutions

Primary care billing is a challenge for many medical practices. Mistakes in coding or a lack of documentation can be costly in terms of revenue and may lead to claim rejection. In 2024, CMS approximated that inappropriate Medicare fee-for-service payments amounted to approximately US $31.7 billion.

The majority of such penalties are related to poor documentation and medical necessity ambiguity. To the providers, this implies that billing should be accurate, adherent, and effective. The article identifies the typical issues in medical billing and provides effective, practice-based solutions that can be applied in clinics on the spot.

Why Billing Is a Pain Point in Primary Care

Primary care practices are characterized by a large number of patients. They provide a great variety of services: preventive care, chronic illnesses, regular check-ups, and occasional procedures. Such a wide area, along with a lack of time per visit, preconditions billing errors.

This complicated workload increases the chances of mistakes. To top the already changing payer regulations, manual workflows, and huge administrative burdens, makes it easy to cause errors.

A single slip, like a lack of documentation or misplaced code, can cause denial or postponement of payment. These minor mistakes add up very fast when you take into account the number of claims.

Common Primary Care Billing Issues 

There are numerous billing issues that primary care practices face, which directly impact the revenue, compliance, and patient care when not addressed.

1. Incorrect or Outdated Coding

Using wrong, outdated, or mismatched codes (ICD‑10, CPT, HCPCS) is a leading cause of denials and improper payments. For example, the widely used CPT code 99214, for established outpatient evaluation & management, was tied to over US$564 million in errors in 2024.
In more than 63% of those errors, the root cause was incorrect coding. Around 20.1% had no documentation, and 16.5% had insufficient documentation. 

The common causes are:

• Coders may apply outdated codebooks.
• They may use codes that do not match the service or documentation.
• Modifiers might be missing or misused.
• Coders may misinterpret the complexity of E/M visits or apply unbundling incorrectly.

2. Insufficient or Missing Documentation

CMS’s 2024 stats show that about 68% of Medicare FFS improper payments happened because of poor or incomplete documentation. Among the missing are medical necessity justifications, unsigned notes, missing dates, or missing patient records.

Common documentation gaps include:

• Lack of clear justification of medical necessity.
• Physician signature or oversight omissions.
• Missing treatment plans or progress notes.
• Noncongruent records to billed dates or services as identified by the Medicaid Payment Error Rate Measurement Final Report.

3. Eligibility Verification and Patient Data Errors

Errors in patient demographics, e.g., name, date of birth, or insurance ID, commonly result in denials prior to claims being processed. Also, claims are rejected in case of non-verification of eligibility or absence of prior authorizations. Such administrative mistakes can bring down otherwise sound claims.

4. Late Submissions and Poor Claim Follow-up

Payers typically enforce strict submission timelines. That is often 90 to 180 days from the date of service. If a claim is submitted after this window, it is automatically denied, with no option for reprocessing.

Without a structured follow-up system or denial-management workflow, many denied or unpaid claims remain unresolved. This leads to avoidable revenue loss and delays in reimbursement.

5. High Administrative Burden and Inefficient Workflow

Paper-based operations or disjointed EHR and billing systems increase the chances of typing mistakes in primary care billing. It also causes misplaced claims and delayed claims. Burnout is also caused by the high administrative burden, which reduces accuracy and compliance even more.

6. Under‑utilization of Billable Services & Missed Opportunities

Providers do not charge for all the services they are supposed to charge for (including chronic-care management, preventive visits, care coordination, telehealth (when applicable), or follow-ups). That means they miss revenue and do not fully capture the value of care. 

Due to underutilization, practices might leave money on the table despite their error-free billing being error-free.

7. Complex Payer Rules and Frequent Regulatory Changes

Payers, such as Medicare, Medicaid, Medicare Advantage, and private insurance companies, vary in terms of documentation, pre-authorizations, prior authorizations, modifiers, telehealth, and coverage. 

Busy clinics have a great challenge keeping up with these dynamic policies. Most of the practices do not have systems to monitor updates, resulting in failures to comply or non-compliance.

Solutions: How Primary Care Practices Can Fix Billing Challenges in 2026

Here are practical, actionable steps to reduce errors, increase clean claims, and improve revenue flow.

1. Hire and Train Certified Coders + Audit Regularly

• Hire certified coders (CPC, CCS) who are conversant with ICD-10, CPT, and HCPCS.
• Carry out internal audits on the typical E/M codes, like 9921,4, on regular checklists.
• Provide updated coders with all CPT/ICD changes that occur. 

The steps minimize coding errors, which are the main reason for high-value audit failures.

2. Enforce Thorough, Consistent Documentation Practices

• Standardize documentation templates to consist of chief complaint, examination, medical decision-making, plan, follow-up, and provider signature. 
• Demand the documentation that supports every billable service and that provides the medical necessity. 
• Use EHR prompts to not leave any field, date of service, provider, or note. 

Since 68 percent of improper payments are a result of documentation, this in itself would reduce risk significantly.

3. Implement Eligibility Verification & Clean Patient Data Workflows

• Check demographics and insurance during each visit or before service. 
• Employ real-time eligibility tools that interface with the EHR or billing software.
• Pre-authorize coverage, benefits, and prior authorization. 

These measures will reduce rejected claims caused by errors in data or lapses in coverage significantly.

4. Automate Billing Workflow & Use Integrated EHR + RCM Tools

• Select billing software that is integrated with the EHR. 
• Enable code validation, compliance edits, and claim scrubbing. 
• Automate reminders for submitting claims by payer deadlines. 

Automation minimizes manual errors, expedites submissions, and reduces the administrative burden during primary care billing.

5. Build a Denial‑Management & Follow-up System

• Monitor every claim until it is paid. 
• Flag denials automatically, categorized by cause (coding, documentation, eligibility).
• Designate follow-up, re-file corrected claims promptly, and record outcomes. 

This closes up gaps in revenues and refunds denied claims.

6. Capture All Eligible Services, Maximize Billable Revenue

• Visit the patients to identify the billable services that remain non-recorded in the audit: chronic care, preventive care, telehealth, and follow-ups. 
• Train providers to record and charge for such services. 
• Take EHR prompts or checklists so that no services are unbilled. 

This offsets reduced reimbursement in primary care.

7. Monitor Regulatory and Payer Changes, Stay Compliant

• Get subscriptions to payer bulletins (Medicare, Medicaid) and industry updates. 
• Modify coding and documentation guidelines with every regulatory change. 
• Conduct quarterly training of employees. 

Keeping up-to-date prevents refusals due to outmoded practice or lapses in compliance.

Table: Best‑Practice Workflow for Primary Care Billing

Frequently Asked Questions

1. Does Delaware Medicaid require prior authorization differently?

The prior-authorization regulations of Delaware Medicaid depend on the type of service and provider. A significant number of services require pre-authorization electronically in order to prevent the refusal of claims.

2. How does Delaware’s telehealth billing differ from federal rules?

Delaware has more liberal telehealth billing, and it is reimbursed on par with in-person services due to new 2023 state legislation.

3. Are there Delaware-specific modifiers for billing Medicaid?

Yes. The telehealth and transportation services need to be appropriately modifiable in Delaware Medicaid so that the claims can be made appropriately.

4. What Delaware laws impact primary care billing compliance?

The state of Delaware has high privacy and data security standards, which correspond to HIPAA and further Medicaid reporting standards.

5. How can Delaware practices verify patient eligibility efficiently?

The state provides an online portal where eligibility can be checked in real time and an automatic notification upon the change of coverage, depending on local providers.

Optimize Revenue and Ensure Compliance with Expert Billing Support

Primary care billing errors and denied claims can quietly drain your revenue and distract your team from patient care. But it doesn’t have to be that way. With the right support, your practice can streamline billing, maximize revenue, and stay fully compliant.

At Delaware Medical Billing, we help Delaware clinics handle everything from eligibility checks to claim submission and follow-up. Our team makes sure your billing is accurate and efficient so you can focus on caring for your patients.

Want to make billing easier? Contact Delaware Medical Billing and see how our medical billing solutions can help your practice today.