Functional Medicine vs Naturopathic: Understanding Your Best Health Options

Sep 30, 2025

Functional Medicine vs. Naturopathic Medicine: What’s the Difference?

When choosing between Functional Medicine vs. Naturopathic Medicine, it’s essential to understand not only their similarities but also their origins. Naturopathic medicine came first, establishing the whole-systems, root-cause approach that functional medicine later adapted. Functional medicine, officially founded in the early 1990s with the Institute for Functional Medicine (IFM) by Jeffrey Bland, PhD, built on principles long central to naturopathic medical training.

Both aim to get to the root causes of illness, but their histories, philosophies, and training paths differ. This article explores these differences to help you make an informed decision.

Understanding Functional Medicine

Functional medicine is a modern branch of integrative care developed to give conventionally trained providers (MDs, DOs, NPs, RNs, dietitians, etc.) a framework for practicing more holistically. It was designed to bridge gaps in conventional training by teaching root-cause, systems-based approaches.

Functional medicine emphasizes the interconnectedness of biological systems and often uses advanced diagnostic testing to pinpoint dysfunctions. Its core aim: personalized, patient-centered care that looks beyond symptoms to the underlying imbalances driving disease.

Core Principles of Functional Medicine

• Root-cause focus: Every symptom or diagnosis may be one piece of a larger puzzle, so practitioners look for underlying imbalances across systems.
• Systems biology: The body is understood as an integrated network, not isolated organs.
• Personalization: Treatment plans are tailored based on genetics, biochemistry, and lifestyle.
• Lifestyle medicine: Nutrition, exercise, sleep, and stress management are central pillars.

Functional Medicine Practitioners

Practitioners include conventionally trained providers who pursue certification through the Institute for Functional Medicine or similar organizations. Training is not a separate medical degree, but an additional certification program to layer root-cause methods onto existing credentials.

Treatment Modalities in Functional Medicine

Functional medicine plans often combine:
• Advanced lab testing (genomics, microbiome, metabolic function)
• Clinical nutrition and supplementation
• Lifestyle and stress management strategies
• Occasional use of botanicals or integrative therapies, often alongside conventional medications

Exploring Naturopathic Medicine

Naturopathic medicine is the original whole-systems, root-cause medical model. It emphasizes the body’s innate ability to heal when obstacles are removed and healing processes are supported. This philosophy has guided naturopathic doctors (NDs) since the profession’s formalization in the early 1900s, and even earlier through its European and traditional medicine roots.

Like functional medicine, naturopathic medicine considers the whole person—physical, emotional, mental, spiritual, and environmental factors. But unlike functional medicine, this approach is not an “add-on.” It is the foundation of naturopathic medical training from day one.

Core Principles of Naturopathic Medicine

• Vis medicatrix naturae (the healing power of nature): Supporting the body’s inherent ability to heal itself.
• Treat the root cause: Identify and address the underlying reasons for disease, not just symptoms.
• Treat the whole person: Mind, body, emotions, genetics, lifestyle, and environment are all interconnected.
• Education at its core: A collaborative approach between you and your doctor designed to be empowering.
• Prevention first: Emphasis on education and lifestyle for lifelong health.

Naturopathic Doctors and Their Training

NDs complete a four-year, accredited medical program with training in both conventional sciences and natural therapeutics. Their curriculum includes:
• Anatomy, physiology, pathology, pharmacology, and diagnostics
• Nutrition, botanical medicine, physical medicine, counseling, and lifestyle therapeutics
• Extensive clinical rotations with some also completing post-graduate residencies and specialty fellowship programs

Depending on the state, naturopathic doctors may also be licensed to prescribe pharmaceuticals and perform minor surgeries.

Naturopathic Therapies

NDs use a broad toolkit, often layered strategically, including:
• Advanced lab testing (whole-body assessments (hormones, nutrients, genomics, microbiome, metabolic function)
• Botanical medicine and nutraceuticals/supplementation
• Nutrition and lifestyle medicine
• Mind-body medicine
• Acupuncture and hydrotherapy (depending on scope)
• Prescription medications when necessary, with the goal of minimizing long-term reliance.

Key Differences Between Functional Medicine and Naturopathic Medicine

While both prioritize individualized, root-cause care, the distinction lies in their origins, training, and scope.

Philosophical Differences

• Functional medicine: A certification-based model that integrates systems biology with root-cause thinking. Developed for conventionally trained providers in the 1990s.
• Naturopathic medicine: A full medical system and degree program founded on the philosophy of natural healing, practiced and refined for over a century. Functional medicine was inspired by and built upon this foundation.

Diagnostic Approaches

• Functional medicine: Often emphasizes advanced testing (genetics, microbiome, metabolic panels) and biochemical pathways.
• Naturopathic medicine: Uses comprehensive history, physical exam, conventional and specialty labs/advanced testing (whole-body assessments: hormones, nutrients, genomics, microbiome, metabolic function), plus evaluation of lifestyle and environmental influences.

Therapeutic Strategies

• Functional medicine: Primarily focused on nutrition, supplementation, lifestyle interventions, and integration with conventional medicine.
• Naturopathic medicine: Includes all of the above plus extensive training in natural therapeutics (botanicals, physical medicine, mind-body practices) and, depending on licensure, prescription management.

Choosing Between Functional Medicine and Naturopathic Medicine

Both approaches offer patient-centered, individualized care. Deciding which is best depends on your goals and needs.

If you are seeking a conventional provider with additional root-cause tools, a functional medicine practitioner may fit.

If you want a doctor whose entire medical training is built on whole-systems, natural, and preventive care, a naturopathic doctor may be the better fit.

Integrating Functional and Naturopathic Medicine

In reality, many patients benefit from both. NDs and functional medicine providers often collaborate, each bringing unique strengths. Together, they can provide a powerful blend of advanced diagnostics, natural therapeutics, and integrative care that addresses both symptoms and root causes.

Summary

• Naturopathic medicine came first: A full medical system rooted in natural healing, whole-person care, and root-cause philosophy.
• Functional medicine followed: Founded in the 1990s, inspired by naturopathic and integrative principles, as an advanced certification for conventional providers.
• Both share common ground: Patient-centered, systems-based, root-cause care.
• Key distinction: Functional medicine is an additional training program; naturopathic medicine is an entire medical degree and philosophy from the ground up.

Both offer valuable pathways to healing. The best choice depends on your health goals, the complexity of your conditions, and the type of therapeutic relationship you seek.

If you’re ready to move beyond confusion and piecemeal approaches and truly restore your health, our Signature Offering is designed for you. With the full support of our naturopathic physicians, registered nurses, and functional nutritionists working together, you’ll receive a deeply individualized plan to balance hormones, build resilience, and reclaim your vitality. Ready to talk it through? Book a free 15-minute Discovery Call with Dr. Corina Dunlap to see if it’s the right fit.