How to Create a Clinician Protocol (That Actually Works)
If you’re a CNS or CNS candidate who is trying to organize your process for more streamlined care—you’ve probably realized that having a solid protocol can be a game changer. But what does it really mean to create a clinician protocol? And how is it different from the protocol you give to your clients?
Let’s break it down.
What Is a Clinician Protocol?
A clinician protocol is your professional roadmap. It’s a clinical tool built by you for you—to help you make decisions, stay grounded in evidence, and ensure you're approaching each client with a clear, consistent, and well-informed strategy. Think of it as your master list of “what I might do depending on the person sitting in front of me.”
In contrast, a client protocol is what you actually hand to the client—usually a simple set of 1–3 doable next steps based on what’s most appropriate and realistic for them to implement between now and their next session.
In short:
A clinician protocol holds all the potential tools in your toolbox.
A client protocol selects just the right tool(s) for the job at hand.
Why Create Clinician Protocols?
Creating clinician protocols saves time, reduces decision fatigue, and helps you standardize care while still personalizing treatment. When you sit down with a client and already have a structured understanding of the condition or symptom you’re addressing, you can:
Avoid reinventing the wheel
Identify red flags faster
Feel more confident about evidence-based options
Narrow down the best next steps for your client with ease
Chart in session
What Should a Clinician Protocol Include?
You don’t have to include every one of these sections in every protocol—but here’s a general format that helps keep things comprehensive, organized, and easy to use over and over again.
1. Description of the Condition or Symptom
Start with a brief description of the symptom or condition. This might include diagnostic criteria, prevalence, common clinical presentations, and why a client might bring this concern into session.
Example:
“IBS is a functional gastrointestinal disorder characterized by abdominal pain and altered bowel habits in the absence of observable structural abnormalities. Subtypes include IBS-C, IBS-D, IBS-M, and IBS-U. It is highly comorbid with anxiety, depression, and a history of trauma.”
2. Possible Etiologies or Root Causes
Here’s where you outline potential contributors to the condition. This section is a great way to think functionally—zooming out from diagnosis to systems.
Example for fatigue:
Iron deficiency or B12 deficiency
Sleep apnea
Post-viral syndrome
HPA axis dysregulation
Inflammatory or autoimmune conditions
Mental health factors (e.g., depression)
3. NFPE (Nutrition-Focused Physical Exam) Findings
List any relevant NFPE signs that may appear in clients with this condition. This reminds you what to look for during sessions and helps identify nutrient deficiencies or malnutrition early.
Pro Tip: Add photos of these signs—ideally including examples across different skin tones. Many classic NFPE visuals were created with only lighter skin in mind, which can lead to missed cues in clients with darker complexions. Building a diverse visual reference library not only sharpens your clinical skills but also supports more equitable care.
Example:
Pale conjunctiva → possible iron or B12 deficiency
Glossitis or angular cheilitis → B vitamin deficiencies
Dry skin or brittle nails → potential fatty acid, protein, or zinc deficiency
4. Lab Findings and Interpretation Tips
Include conventional and functional lab markers you might want to order or review, as well as interpretation cues. Highlight the lab ranges that may be more sensitive for early dysfunction versus late-stage disease.
Example for Anemia:
Hemoglobin:
< 12 g/dL (women) or < 13 g/dL (men) → diagnostic for anemia
Ferritin:
< 30 ng/mL → suggests iron deficiency (even if hemoglobin is normal)
Serum Iron:
< 60 µg/dL → possible iron deficiency
Transferrin Saturation:
< 20% → often seen in iron deficiency anemia
TIBC (Total Iron Binding Capacity):
Elevated in iron deficiency
MCV (Mean Corpuscular Volume):
< 80 fL → microcytic anemia (likely iron-related)
> 100 fL → macrocytic anemia (may suggest B12 or folate deficiency)
5. Drug/Nutrient Interactions
Use this section to flag any known interactions that could impact nutrient absorption, medication efficacy, or client safety. This can help guide both your nutrition plan and coordination with prescribing providers.
A. Common Drug–Nutrient Interactions
These are interactions where a medication may deplete, interfere with, or require increased intake of certain nutrients:
Metformin → May lower B12 levels (monitor annually; consider supplementing if low or borderline)
Diuretics (e.g., furosemide) → May lead to losses of potassium, magnesium, and thiamine
Statins → May reduce CoQ10 levels; consider 100–200 mg/day CoQ10 if fatigue or muscle pain present
ACE inhibitors → Can increase potassium levels; use caution with high-potassium diets or supplements
Viagra → grapefruit can increase bioavailability, potentially leading to increased side effects
6. Nutrition Recommendations
Use this section to outline your evidence-informed nutrition strategies for the condition or symptom you're addressing. Aim to include:
Foundational nutrition practices – such as eating regularly, supporting blood sugar balance, and ensuring adequate protein intake.
Targeted nutrition interventions – including macronutrient adjustments (e.g., increasing protein for wound healing), micronutrient repletion (e.g., iron for anemia), and any foods or patterns shown in research to be beneficial.
With micronutrient repletion, be sure to indicate potential nutrient/nutrient interactions
Calcium and iron → Compete for absorption; take supplements at different times of day
Zinc and copper → High zinc intake can deplete copper; maintain a 10:1 ratio or supplement copper if zinc exceeds 40 mg/day
Folate and B12 → Folate can mask B12 deficiency symptoms; ensure adequate B12 when supplementing folate
Vitamin D and magnesium → Magnesium is a cofactor for vitamin D metabolism; low magnesium may reduce the efficacy of vitamin D supplementation
Therapeutic dietary patterns – such as Mediterranean, low-FODMAP, or anti-inflammatory approaches where appropriate.
Specific foods studied – for example, turmeric for joint pain or kiwi for constipation.
Example
Condition: Iron-Deficiency Anemia
Dietary Pattern: Focus on a nutrient-dense, omnivorous or flexitarian diet with a variety of iron-rich foods and enhancers of iron absorption
Macronutrient Emphasis:
Ensure sufficient protein intake (especially heme iron sources like beef, poultry, and fish)
Micronutrients:
Prioritize iron (heme and non-heme sources), vitamin C (enhances absorption), and monitor intake of calcium and phytates (which may inhibit iron absorption)
Individual Foods to Include:
Heme iron: beef, chicken liver, clams, sardines
Non-heme iron: lentils, tofu, quinoa, spinach (note lower bioavailability)
Vitamin C-rich foods: oranges, bell peppers, strawberries
6. Supplement Considerations
This section is for you—not your client—to organize potential supplement strategies. List evidence-based options, common dosing ranges, preferred forms, timing (e.g., morning vs. evening), and any key safety considerations. Be sure to flag supplements that may be contraindicated with medications.
Also—save yourself time later by listing multiple delivery formats for each supplement wherever possible. If magnesium glycinate is your go-to, make sure you note whether it’s available as a capsule, powder, liquid, or gummy. This will come in handy when you’re working with clients who can’t swallow pills, have taste aversions, or need a format they can sneak into a smoothie. If you see kids or teens, make sure to also include proper dosing for their age/size.
Example for mood support:
Magnesium glycinate: 200–400 mg in the evening; calming and well tolerated
Pure Encapsulations Magnesium Glycinate Capsule, 1 capsule = 120 mg
Pure Encapsulations Magnesium Glycinate Liquid, 2 tsp = 165 mg
Thorne Magnesium Bisglycinate Powder, 1 scoop = 200 mg
7. Lifestyle Recommendations
Think sleep hygiene, movement, breathwork, or other nervous system tools.
Example for PCOS:
Gentle movement post-meals (like a 10-minute walk)
Focus on sleep regularity, not just hours
Avoid over-restriction—support blood sugar and the nervous system
8. Client Handouts or Education Materials
This is a living list of client-friendly tools that pair with the protocol. Include links or titles to handouts, guides, or recipe packets you've created.
Example:
“Blood Sugar Basics” handout
Low FODMAP Phase 1 Overview
Gentle Nutrition Tracking Template
9. Relevant Guidelines
If there are clinical guidelines or position papers relevant to the condition (e.g., from gastroenterology associations, ASPEN, or other specialty associations), include links or notes here. Even if you practice functionally or integratively, it’s helpful to anchor to existing standards of care.
10. Trainings, Webinars, or CEUs
Finally, keep track of any CEUs or expert trainings you’ve taken—or want to take—on this topic. This section is a great place to keep track of papers and studies that you haven’t yet read about the condition - but want to save to read later.
Example:
Monash University IBS Training
Osher Center Handouts for Chronic Pain
FODMAPs alter symptoms and the metabolome of patients with IBS: a randomised controlled trial
Putting It All Together
Creating a clinician protocol isn’t about following a script—it’s about building a clinical framework that helps you stay grounded in complexity without getting overwhelmed. It gives you a home base of evidence, experience, and structured thinking to pull from, so you can make more confident and tailored decisions for each unique client you serve.
Whether you create your protocols in a Google Doc, Notion, an EHR template, or a big binder on your desk, make them work for you. And don’t forget—they’re living documents. Revisit and revise them regularly as new research emerges and as your own clinical skills evolve.
💡 Pro Tip: Always cite your sources or hyperlink to the studies, guidelines, or resources you’re referencing—even if it feels like overkill. This isn’t school, and no one is grading your work—but two years from now, when you're wondering where the "2 kiwis a day for constipation" recommendation came from, you'll be really glad you saved the link. Tracking your references also makes it easier to confidently update protocols, educate colleagues, and support your reasoning in supervision or case reviews.