How to Successfully Integrate AIP into a Conventional Healthcare Setting

This post comes from AIP Certified Coach Lori Beeken, who works in the acute care setting as a Registered Dietitian. She is fortunate to work in an environment where western medicine physicians promote nutrition, lifestyle, and alternative medicine in addition to conventional medical and surgical options. We were curious to know what it looks like patient-to-patient to use dietary interventions as a tool in the treatment toolkit, what the biggest challenges are, and what makes her clinic such a successful example of this. 

Hello AIP community! My name is Lori and I am a Registered Dietitian that has been working in the acute care setting for the past 14 years. I specialize in nutrition therapy for gastrointestinal disorders and have recently expanded my practice to the outpatient arena where I am fortunate enough to work in a very progressive Gastroenterology Clinic at Scripps Health in La Jolla, California. I work under the guidance and support of Dr. Gauree Konijeti, gastroenterologist and Director of the Inflammatory Bowel Disease (IBD) program at Scripps Clinic. In my nutrition practice, I see patients with inflammatory bowel disease, including Crohn’s disease and ulcerative colitis, but also a wide variety of other autoimmune and gastrointestinal diseases.

Until I became aware of the Autoimmune Protocol certified coaching program, conventional medicine had formed the basis of my knowledge of nutrition therapy. Becoming an AIP Certified Coach has not only broadened my knowledge of non-traditional and alternative therapies, it has shown me how effective diet and lifestyle changes can be at helping to control underlying inflammation, therefore, alleviating the detrimental effects of chronic disease.

I feel fortunate to work in a setting in which traditionally trained, western medicine physicians promote nutrition, lifestyle, and complementary and alternative medicine in addition to conventional medical and surgical options. The doctors that I am lucky enough to work alongside are extremely supportive and understand the efficacy of nutrition therapy in the treatment for autoimmune disease. We share similar goals for our patients by promoting autonomy through healthy diet and lifestyle changes to support gut health and improve overall well-being.

Our individual diet therapy focuses on working with specialized diets that best fit our clients’ metabolic and digestive needs as well as lifestyle habits. We make use of a variety of elimination diets, exclusive enteral nutrition (EEN), and in some cases when oral intake is not feasible, enteral (tube feeding) or parenteral (intravenous) nutrition. We routinely monitor for micronutrient deficiencies and offer guidance on supplementation as needed. Elimination diets like AIP, can be modified as needed to best suit our patients’ current health conditions and nutritional status.

The AIP diet provides an excellent framework from which to provide nutrition therapy – modifying and adjusting nutrient load based on individual needs and current health conditions. For example, if a patient is experiencing an acute flare, we may need to rely very strictly on nutrient dense liquids and extremely bland, low fiber, well-cooked foods to ease bowel function. In contrast, if someone is in remission, feeling well and having achieved more regular bowel patterns, we are able to liberalize their diet, encouraging a wider variety of foods including raw vegetables and fibrous meats. If a patient presents very malnourished, I often find maintaining an easy-to-digest, staple carbohydrate in the diet, such as white rice and/or potatoes rich in soluble fiber, is essential for providing alternate substrate for weight maintenance and even gradual weight gain.

Part of our diet education includes understanding the process of digestion. I explain that the first stage of digestion takes place in the cooking process. By cooking, steaming, roasting, chopping and pureeing we are breaking down the structural component of the food itself, therefore aiding digestion and absorption of nutrients as the food travels through the GI tract. This concept is particularly important for our clients that have prior surgical history, with remnant strictures or adhesions, placing them at increased risk for bowel obstructions.

As integrative health professionals, our role is to not only educate our patients on nutrition, but also to outline how optimizing a healthy mind, body and soul is essential to managing current illness and preventing further progression of disease. We work to identify confounding variables that may be contributing to underlying inflammation; addressing sleep, STRESS, and exercise patterns. Stress significantly impacts the course and well-being of our patients with autoimmune disease. I tell my patients, that regardless of how impressive our dietary changes are, if they are unable to control underlying stress in their lives, they will still struggle with uncomfortable and persistent gastrointestinal symptoms. Finding an outlet for stress, whether it be through meditation, yoga or other moderate physical activity, prayer, journaling or artwork, can be extremely powerful “medicine” and profoundly alleviate symptoms.

Perhaps the most challenging part of a nutrition assessment is targeting a patient’s willingness and readiness to adapt to a new therapeutic diet. Most often, our patients are very sick, have either undergone intense surgical intervention in the recent past or are on several medications to keep their underlying illness under control. I find that nutrition is perhaps the one thing that they hold tightly to and feel the most in control of. This notion can lend itself either to strong-armed resistance or enthusiastic acceptance to change one’s diet. Understanding your patient’s personality and how they will be most successful with their dietary changes is of utmost importance. Furthermore, understanding how realistic these diet and lifestyle changes are from a financial and accessibility perspective is equally as important. Fortunately, there are several resources provided on the autoimmune wellness website that help make the AIP lifestyle applicable to people from all economic and social backgrounds.

We spend most of our time in our sessions discussing the nutritional value we are adding to our patients’ diets, rather than focusing on what foods they are eliminating. Nutrient density forms the basis of our nutrition therapy discussion. Understanding the value that nourishing foods offer to our biological and physiological systems can help our patient’s feel more in control of their own bodies and their overall healthcare. It can give them the “Why” that they are searching for to make these diet and lifestyle changes. Whether they are more inclined to jump head-first into these nutritional interventions or slowly and gradually work out the dietary “kinks” along the way, providing a perspective of food as a nutraceutical can be transformative. Important information that is gathered in our nutrition assessments can then be brought back to the physician, offering an interdisciplinary approach by providing an alternate perspective and personal insight. This collaboration between physician and dietitian can vastly improve patient care.

The ultimate goals of nutrition therapy for our patients with autoimmune disease affecting their GI tract include decreases in inflammatory markers, increased intestinal absorption of micronutrients (vitamins/minerals), increased protein stores and preservation of lean muscle mass, as well as increased energy level and improvements in overall well-being. In order to achieve these goals, we aim to maintain the most liberal diet with the absence of uncomfortable symptoms.
I have found AIP to be a powerful tool for our clients, allowing them to feel empowered and confident that they have a hand in determining the course of their healing journey. Although nutrition therapy in autoimmune disease has often been overlooked, I am witnessing firsthand the powerful impact that nutrition therapy and diet education has on not only those affected by disease, but also those treating it as well.

About Lori Beeken

Lori is a Registered Dietitian from sunny San Diego, California. She is a mama of two beautiful girls, Lucy (9 years) and Riley (5 years), a wife to a basketball and golf-loving husband, and an avid runner. She loves to spend her free time in the kitchen baking healthy treats for anyone courageous enough to try them! Lori has been working in a conventional medicine setting for the past 13 years, specializing in gastroenterology, and has been able to use her AIP coaching to not only help her patients with Inflammatory Bowel Disease and a variety of other gastrointestinal disorders, but also to educate other healthcare providers on the efficacy of nutrition therapy in autoimmune disease. When she’s not working, you can find her chasing her kids around the soccer field or chasing waves at the beach. 


  • Kimberly King says

    I love it:
    “We spend most of our time in our sessions discussing the nutritional value we are adding to our patients’ diets, rather than focusing on what foods they are eliminating.”

  • Debra says

    Thank you for the great read, I am in Florida. I am relying on the support groups, so I don’t go on this journey alone. I’ve been on the AIP protocol for two days now. I’m having trouble finding information regarding certain foods that I’m not sure I can eat for instance protein powder I’ve always enjoyed a protein drink in the morning. As well as I’m a caffeine lover. Decaffeinated herbal tea is not doing it for me. I guess my only option is decaffeinated coffee but I’m afraid to drink it I don’t want set myself back.
    Do you have any suggestions for me. Much appreciated, have a great day.

    • Angie Alt says

      Hi Debra-
      Most protein powders are out on AIP, as they include legume based proteins. You might check out Vital Proteins for some collagen based powders you can add to smoothies. AIP is not a no caffeine protocol, but it is a no coffee protocol. We eliminate coffee, because it is a seed, not due to caffeine. You can sub in caffeinated teas (be sure there aren’t other ingredients that are out on AIP), but do practice good self-awareness. For some it is worthwhile avoiding caffeine, especially early in the healing process when you may be experiencing some blood sugar dysregulation. You can learn more about what is in or out & why in this blog post:

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