Combining AIP with Conventional Healthcare: The Definitive Guide

A little clarity… I’m specifically exploring the whats, whys, and hows of combining AIP with conventional healthcare here. I realize that much of what is outlined could also be accomplished with natural or functional practitioners, but due to insurance restrictions, legal regulations in some states, or financial limitations, many people are not able to utilize natural or functional medicine. The purpose is not to overlook those options, but instead to demonstrate what can be accomplished within the conventional healthcare landscape when AIP is also used. Additionally, I hope to show that in cases where you are working with natural or functional practitioners, but they too are recommending utilizing conventional treatments, it can be still be a win in your AIP journey.


If you have an autoimmune disease or are close to someone with an autoimmune disease, it’s probably obvious to you that combining multiple approaches, such as diet and lifestyle protocols like AIP with medication, is absolutely necessary for the best possible management of the disease. Autoimmune diseases are complex and change over time, with periods of seeming remissions and then dramatic flares. If you’ve had to personally navigate the ups and downs of chronic illness, it usually doesn’t take long to recognize that every tool or combination of tools is worth trying.

Unfortunately, combining your options is much easier said than done, because our current healthcare model is not built with chronic illness in mind. It is up to you to advocate for this approach, but I know (from personal and professional experience), that it’s daunting. I’ve written this guide to clarify the process and hopefully help you get the most out of all the options.

Does turning to conventional medicine mean failure?

Before I jump into the practical steps required to combine AIP with conventional healthcare, there’s a very, very important point that must be made in no uncertain terms. Needing medication, surgery, or any other type of conventional healthcare in order to achieve your highest level of personal wellness, despite your autoimmune disease, is not failure. It’s smart! There is no one best way to manage an autoimmune disease, but comparing your journey to another’s is definitely the best way to prevent yourself from enjoying health and happiness now.

Okay, with that important point out of the way we can continue.

Terms: What qualifies as “conventional” and what are the other options?

Making informed decisions about combining AIP with conventional healthcare is easier if terms are clearly defined. There’s a lot of confusion on different forms of medicine, because sometimes forms overlap or differences are subtle. Below you’ll find a reference guide.

  • Conventional medicine: “A system in which medical doctors and other healthcare professionals (such as nurses, pharmacists, and therapists) treat symptoms and diseases using drugs, radiation, surgery, etc. Also called allopathic medicine…” (1)
  • Naturopathic (natural) medicine: “Naturopathic medicine emphasizes prevention, treatment, and optimal health through the use of therapeutic methods and substances that encourage an individual’s inherent self-healing process.” (2
  • Alternative medicine: when a nonconventional (alternative) treatment is used instead of a conventional one
  • Complementary medicine: when non-conventional and conventional treatments are used in conjunction
  • Integrative medicine: similar to complementary medicine, but executed in a coordinated way
  • Holistic medicine: when a healing modality addresses the whole person, physically, mentally, and spiritually, instead of that person’s parts
  • Functional medicine: similar to holistic medicine, but focuses on discovering the root causes of disease, using a systems-oriented approach, engaging both patient and practitioner in partnership, and utilizing both conventional and natural treatments. (3

Practitioner Types: Who can I partner with?

There are licensed and medical practitioners in both conventional and natural medicine, but in this guide, we’ll be focusing on conventional. “Licensed” means a medical school graduate has met the requirements of a government approved professional association or a government agency to legally practice medicine in a certain area. “Medical” used here is in reference to a practitioner’s qualification to diagnose and treat disease, including prescribing medication. Below you’ll find a reference guide to licensed, medical conventional practitioners.

  • MD (Medical Doctor): has completed medical school, generally 4 to 6 years after completing a bachelor’s degree, and often also completes a residency lasting at least 2 years, passes an exam to acquire license, practices general care (internal medicine, family medicine, or pediatrics) or specializes in a body system
  • DO (Doctor of Osteopathic Medicine): very similar training to an MD, but there is more emphasis on primary care education, a whole-body approach, preventive care, the musculoskeletal system, and manipulative treatment
  • PA (Physician Assistant): training takes 2 to 3 years to complete, much less than an MD, but similar in scope, works under supervision of an MD.
  • NP (Nurse Practitioner): an RN with advanced education and training, including a graduate degree and rigorous work experience, in many places can practice without MD supervision

If you’re interested in learning more about licensed, medical natural practitioners (who are also able to diagnose and treat disease, often including prescribing medication) and/or non-licensed, non-medical practitioners who can play a supportive role on your healthcare team, grab a copy of our book, The Autoimmune Wellness Handbook. We dedicate an entire chapter to this topic.

Benefits: Why would I combine AIP with conventional healthcare?

Now that we’ve clearly defined conventional medicine and other forms of medicine, as well as clarified who typically practices in the conventional space, it’s time to explore the reasons you’d consider combining AIP with conventional healthcare in the first place. The list below makes a clear case for combining.

  • AIP may help conventional treatments work more effectively. AIP can help lower inflammation, address nutrient deficiencies, improve blood sugar regulation, and correct hormone balance. There is both anecdotal and research-based evidence that addressing these foundational issues may allow medications to have a greater impact. Note that in the first-ever AIP medical study, many of the participants were on drugs for inflammatory bowel disease, but it was not until adding AIP that they were able to achieve remission.
  • Your conventional practitioner can order and interpret testing that may help direct your AIP process or serve as a way to monitor progress. Some providers are willing to use newer, functional forms of testing, but many do not. However, that doesn’t mean that they can’t provide you valuable information with conventional testing (which is also more likely to be covered by insurance!). For example, with blood testing they could monitor changes in inflammation markers, antibody levels, blood sugar levels, hormone levels, cholesterol levels, liver function, and even nutrient status, among other things, that provide important clues to what you should focus on with AIP, where tweaks could be made, or what is working. This doesn’t even account for other forms of testing, like imaging, that might reveal even more information to help you and your provider partner on your AIP journey. For example, if your provider notices your iron levels are low, you might focus on more organ meat or if inflammation markers are improving your provider might encourage to continue your focus on omega-3 rich fish.  
  • Your conventional practitioner can determine if decreasing or discontinuing medications is possible once you’ve adopted AIP. Decreasing or weaning off medications safely can only be done with your provider’s guidance. She can determine if and when AIP has made that possible, for example, by monitoring your thyroid and decreasing medication if AIP improves hormone levels.
  • Your conventional practitioner can help you decide if some treatments (like surgery) can be delayed or avoided with the help of AIP. If your autoimmune disease requires surgery, your doctor is qualified to monitor you and help you confidently determine whether timelines can be lengthened or if this serious step can even be avoided. For example, through colonoscopy your provider might determine that your Crohn’s is improving and decide to delay a surgical decision.
  • There may be underlying issues that require treatment beyond what AIP can address and your conventional practitioner can help in those cases, so that those issues do not prevent progress. There are many potential underlying issues that your provider might be able to diagnose and treat that changes in your diet or lifestyle won’t fix. For example, I’ve worked with many clients who made much greater progress on AIP after their providers identified and treated bacterial infections that were plaguing them.  
  • If there are any aspects of AIP that are contraindicated in your case, a conventional practitioner can clarify that and possibly recommend modifications. Talking to your provider about your decision to make diet and lifestyle changes is smart, since they may have insight about your individual case and know if some aspects of AIP aren’t right for you. For example, AIP is not intended to be a high-protein diet, but protein intake may need to be adjusted for those with autoimmune kidney disease.
  • A successful partnership with a conventional practitioner can empower you on your AIP journey. A great working relationship with your provider can help you make diet and lifestyle changes successfully, since you’ll have the support and expert guidance to take each step with confidence.

Timing: When should I consider combining?

The simple answer is now! The benefits outlined above are so clear. Just going it alone and hoping AIP addresses all your problems is not usually enough when it comes to autoimmune disease. As I said at the start of this article, autoimmune disease is chronic, complex, and changing, so why not start using every tool to address it right away!?

That said, here’s some more specific guidance on when to combine:

  • You want to try AIP, but suspect aspects of it may not be right for you and you’d like more clarity. Your provider hopefully knows you and your health history well. Make an appointment to chat with her about AIP and ask her specifically to address any of the aspects you aren’t sure are right for you or if she notes anything that could be an issue after learning about AIP.
  • You’ve tried all the conventional options, but you aren’t feeling better and your provider is out of ideas. If this is your situation, it’s time to consider what you can do by making changes to your diet and lifestyle to help manage your autoimmune disease. Tell your provider about AIP and ask them to partner with you to see if it can help you get past the barriers to health and wellness that the conventional options haven’t been able to fully address yet. If you can both remain open-minded and see this as an experiment with the only real downside being “eat more nutritious food,” you may just find that AIP alone works or AIP plus the conventional options is more effective in your case.
  • You’ve tried AIP on its own, but you aren’t making the progress you expected. If you’ve been fully compliant with the elimination phase of AIP for 90 days and you still don’t feel noticeably better or improvement has been very minimal, it’s time to consider what you can achieve by adding conventional approaches to managing your autoimmune disease. Tell your provider all the effort and time you’ve put into dietary and lifestyle changes and ask him to partner with you to either discover if their underlying issues that need treatment or if adding medication might be the powerful combination you required.
  • AIP was working well, but you seem to have hit a plateau. Sometimes improving our diets and lifestyles has an enormous impact on our autoimmune diseases initially, but over time it doesn’t seem to be enough despite our best efforts. Maybe you’ve entered a new life stage and your body is shifting? Maybe factors outside your control are limiting the effectiveness of AIP? Whatever the reason, this is a good time to see your provider and ask him if it’s time to consider adding new conventional options. A really positive example of a journey like this is Eileen Laird’s story at Phoenix Helix.

Risks: What about all those times conventional healthcare failed me?

At this point in this post I know a lot of you are thinking, “That’s all great, but conventional healthcare has failed me. My provider would never support me.” I deeply understand and validate that reaction. I’ve had so many bad experiences with conventional healthcare during my journey with autoimmune disease, especially in the early stages when I didn’t have a diagnosis yet. It was frustrating and hurtful. After diagnosis and adding AIP, I still had a few interactions that were disappointing… to say the least. However, over time I realized three things that have made my experience with conventional healthcare more positive:

  • Conventional healthcare excels in important ways and I am lucky to benefit. For instance, while there are always risks with surgery, to a great degree the surgical treatments that exist right now are miraculous breakthroughs in human health and the conventional system is designed for this kind of intervention. I am so lucky to have that option if I need it!
  • I am the boss of my journey. I am not solely blaming myself for any failures that occurred during my attempts to get help through conventional healthcare for my autoimmune diseases. There were glaring mistakes made by multiple providers that delayed my return to health by years. However, I can now see that there were also missteps on my part, and I was expecting providers to offer much more than is realistic. AIP helped me embrace a new level of personal responsibility for my health and well-being and the side effect was adopting a very empowered stance with my providers. In most cases, that empowered stance turned our relationship into a partnership and care was much more effective.
  • The system is flawed, and providers suffer too. Almost everyone in the US now agrees that our mainstream healthcare system is at some level broken. Among other issues, we have an epidemic of chronic illness, but a system mostly designed for acute issues. Regardless of what you see as the contributing factors, it should not be overlooked how much it is also impacting our providers. They are under enormous stress to play all roles for their patients in smaller and smaller time slots for less and less money while being asked to pursue a grueling education and stay on top of research and advancements for a lifetime. This article by Chris Kresser details just how serious the problem is, leading to severe burn-out and sadly, even suicide. I keep all this in mind when utilizing conventional healthcare, so that I can focus on accessing the best parts it offers and approach my provider relationships with the same empathy I am hoping to receive.   

Combining: How do I actually combine AIP and conventional healthcare?

And now we finally come to the meat of this topic. But how exactly do I do this? The truth is that navigating this process will be different for each individual. It will depend on you, your resources, your diagnosis and current level of health, the willingness of your providers, and the limitations they face. The following are a few practical tips to give you the best chance of successfully combining or to get the conversation starter with your provider.

Embrace your role and be realistic. You are the MVP on this team, do not shy away from taking full responsibility for that role. You are likely to be the coordinator of information between providers, you hold the key details about yourself, and if you want your provider to respect what you are doing in terms of AIP, you need to treat it seriously. In this same vein, be realistic about what your provider can do for you. If the partnership is productive, but there are aspects of your care he can’t meet, don’t throw out the baby with the bathwater. Add members to your healthcare team that can play a support role. For example, your provider agrees that AIP is smart, but is not be able to teach you how to practically transition to the diet. In this case a coach, like those we’ve trained through AIP Certified Coach, can fill that role.

Whether your provider is supportive or not, they need to know about your diet and lifestyle. I have seen this first hand many times, including in a research setting, AIP is powerful enough to impact future healthcare decisions and you don’t even give your provider an opportunity to collaborate if you haven’t given them all the information.

If your provider is not supportive, as them to clarify their concerns. This doesn’t have to be a confrontational exchange, just ask respectfully what parts of AIP raises alarms for her. AIP is a template that can be modified and perhaps she has some valid concerns in your specific case and there is opportunity to work on modification together.

Educate your provider about AIP. Like I mentioned earlier, providers are expected to take on a nearly super-human level of study. It’s not reasonable for them to be fully informed on every single advancement or piece of research. Share books with ample citations like The Paleo Approach or The Autoimmune Wellness Handbook or the results of the first efficacy study. Maybe he’d love to learn about this option, not just for you but for his other patients struggling with autoimmune disease, but just doesn’t have enough hours in the day to search out the information. Be sure you approach this without condescension, but instead with a spirit of sharing valuable information.

Establish milestones. If you and your provider are on the same page, the next step is to talk about future healthcare decisions. As mentioned, AIP can change the course of things a lot. Ask your provider if more frequent monitoring can be set-up and what sort of milestones will indicate to her that medication or other changes to your treatment can be attempted.

Always practice full transparency. If you don’t trust your provider enough to be open about what you feel is happening with your health and the steps you are taking personally, for instance adopting AIP, to try to improve your health, that is a huge red flag that you will not have a successful partnership. It’s better to move on and keep looking for a good fit (as exhausting as that search can be!) if this is the case for you.

I hope this article convinced you that combining AIP with conventional healthcare is not only possible, but also addressed the whats, whys, and hows of taking that step thoroughly. The goal is your highest wellness, autoimmune disease and all. You deserve that and shouldn’t give up on that ambition over perceived limitations working with conventional healthcare. There are amazing medications, cutting-edge surgical techniques, and deeply committed providers within this form of medicine and using all the best that it has to offer, along with all you can do for yourself through diet and lifestyle is likely to be the best way forward. And it’s certainly not a failure! It’s smart!

About Angie Alt

Angie Alt is part of the blogging duo behind Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with Celiac and other autoimmune diseases; one creative, nutritious meal at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She’s also a world traveler who has been medically evacuated from two foreign countries. Strategizing worst-case scenarios is now something of a hobby. She is a Certified Health Coach through the Institute for Integrative Nutrition and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol. You can also find her on Instagram.

14 comments

  • Kathleen says

    Thanks for writing and sharing this article. I appreciated your emphasis on being realistic about what a conventional doctor can provide given the many, many demands on their time. I have found expressing gratitude can also go a long way towards establishing a partnership. I was hospitalized last winter after a flare of my Crohn’s disease (I started AIP after I got home) and sent a thank you card to my doctor and his medical assistant for all their help and support during a very difficult time. They both mentioned to me how much they appreciated it the next time I saw them, and I feel like it has helped me developed a deeper relationship with both of them. If it feels appropriate, I’ve even had short conversations with them about their own lives (my doctor and I are about the same age and we both have young kids, his medical assistant was out on sick leave for a while and she shared just a bit about what was going on). I know this probably can’t happen with all providers and certain boundaries are important but expressing gratitude and an interest in them as people can also be really helpful sometimes.

    • Angie Alt says

      I totally agree Kathleen! Thanks for sharing!

  • Anna Dugan says

    You mention two books and a study to cite to your conventional provider. A short list with links or citations of the most convincing studies and current research for skeptical/traditional providers would be so helpful. My dermatologist is still adamant that diet doesn’t help at all.

    • Angie Alt says

      Anna-
      When the words in the post are a light blue color, it means you can click on them & be taken to the book, study, resource, etc. that is cited. You’ll be able to find everything for your Derm by clicking them.

    • Mickey Trescott says

      Hi Anna! We’d encourage you to check out The Paleo Approach, the book by Sarah Ballantyne that has over 2,000 scientific references for the AIP recommendations. It is great for starting conversations with your provider.

  • Jul says

    Great article! I’ve had tons of success combining AIP with conventional meds, and am now finally in the process of slowly reducing the meds under my doc’s supervision. My followup question is this: How do you navigate reintroductions on AIP while on conventional meds. Does medication (immunosuppressants) skew the reintro results? I ask because I’ve had a suspiciously good success rate with reintros and it makes me skeptical that my reactions are being suppressed—although I did have one definitive “no” reaction. I will note that I’ve been on AIP for four years and waited at least two years before starting reintros (I’ve heard some say “don’t start reintros until you’re off medication” but that obviously wasn’t going to be viable for me since AIP isn’t designed to be forever). I’d love to hear your thoughts! Thanks again for putting together such a wealth of AIP resources. 🙂

    • Angie Alt says

      Jul-
      It could be possible that the medications are suppressing reactions, but if some medication is going to be part of your picture always or at least for a considerable length of time as you wean down, it may be worthwhile to continue. You might discover later that you need to retest a few of those foods.

  • I would love to find an MD associated with our insurance provider who can handle me having a functional practitioner also on my team. My current MD is hostile and suspicious, and cannot support the treatments my Lyme practitioner provides or my ND who is managing my hormonal imbalances autoimmune disease, adrenal dysfunction and GI dysbiois. Nothing either does makes her happy, and I would go elsewhere for both our sakes. How do I find someone not so antagonistic?

    • Angie Alt says

      Diane-
      It will take trial & error, but if your doctor is openly hostile about your working w/ an integrative team I would definitely consider moving on.

  • Cindy Brown says

    Thanks so much for publishing this article, Angie. Not so much for my own autoimmune disease but for my 13 yo daughter, who was diagnosed with juvenile idiopathic arthritis last year. I have struggled trying to get her to follow the AIP diet – it’s the one thing through all of the pain and swelling and limping around for months on end – that made her cry. Not self administering methotrexate or adding in Humira (that made me cry) but not being able to eat pasta and pizza. We have found a lot of good gluten free pasta and some decent pizza and she’s eating tons of fruits and vegetables (she’s a vegetarian) but I have felt like a failure as her mother in not doing more to keep her off of those drugs. And while her doctor is wonderful, she doesn’t think changing her diet will “do much,” which is exactly what my daughter wanted to hear. I felt such relief and gratitude when I read “Does turning to conventional medicine mean failure?” And I’ve started the AIP diet TODAY, in hopes that I can be an example to her. Thank you so much – you’ve given me the encouragement I needed!

    • Angie Alt says

      Cindy-
      I’m so glad this was encouraging & I’m so sorry that your daughter is struggling. I know that is hard on a mama’s heart. A few things:
      1. Often, despite autoimmune disease, kids don’t need to go as far on the AIP template as an adult would. They just haven’t had as long for their diseases to do damage & sometimes can get very positive results w/out as much restriction. The goal is always the least restrictive diet that provides the individual w/ the greatest health.

      2. If she is vegetarian, the first thing I might do is work w/ her on the possibility of doing pescatarian AIP, meaning she will add fish & seafood. AIP + vegetarian is not nutritionally sound, as plant sources of protein are removed. The next thing I’d do is work w/ her on a slower & less restrictive AIP template (maybe see if she can tolerate gluten-free grains, some of the nuts & seeds, etc. that can open up her options some). That might help her feel more able to sustain it w/ less psychological loss.

      3. The most successful AIP kids have supportive households. Thanks so much for being willing to work on it yourself as an example for her.

  • Anni says

    Hey! I’ve been doing AIP since August. I feel a lot better but I just had a bunch of tests done and the results were not that good. My bad cholesterol (LDL) has spiked to 3.9 mmol/l (should be max 3.0). Also my HDL has increased to 2.5 and triglyseride is 0.76. So my total cholesterol is 6.9 when it should be under 5.0. I haven’t eaten a lot of “bad fats”, but because I’m underweight, I’ve eaten a lot of coconut products and I’m wondering if that’s the reason. Also my TSH has dropped to 0.14, when it used to be around 0.5 (I’m not on thyroid medication but I do have a goiter). I’m really confused cause I feel a lot better but the tests tell a different story… 🙁 I tried to find information about AIP and cholesterol, but didn’t find much. I know you can’t give any medical advice but I was wondering if you have any good tips where to find info about AIP and cholesterol? And also, can the diet affect the thyroid this much or is it just a coincidense?

    • Angie Alt says

      Anni-
      We aren’t doctors, so we can’t give medical advice. A very good resource to help you understand cholesterol is Chris Kresser’s website. Do some googling of cholesterol+chris kresser for solid info. Your HDL going up is actually good, it is protective. As to the how powerful the diet is, we’ve definitely seen it impact thyroid numbers. If you feel great, don’t let the numbers alone alarm you. Discuss them in context w/ how you feel w/ your healthcare providers.

      • Anni says

        Hi Angie! Thank you for the reply. Yes, HDL is good and my number is reaaally good. Just the high LDL is confusing… Of course, I understand you can’t give medical advice. Thank you for the tip about Chris Kesser, I’ll do some googling! And thank you so much for the great work you do! AIP has been life changing 🙂

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