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What to Do When Elimination Diets Don’t Work. A Talk with Jennifer Fugo

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What to Do When Elimination Diets Don’t Work. A Talk with Jennifer Fugo

Do elimination diets really work? And if so, why did my elimination diet fail? This is a question I get asked a lot, from people who wonder why the AIP or other elimination diets don’t work for them. In this exclusive interview with functional clinical nutritionist Jennifer Fugo, we are going to dig deeper into this topic and help you find an answer to that question, as well as give you practical tips that you can implement right now to try and steer your healing process in the right direction.

Speaking from my personal experience, I am always extremely grateful that I found out about the Autoimmune Protocol (AIP). I won’t hide that it was really hard, but luckily I was able to stick to it and reap great benefits. However, going on an elimination diet wasn’t the only tool I used during my journey, and the other pieces of my healing puzzle were just as important.

What to Do When Elimination Diets Don’t Work. A Talk with Jennifer Fugo 3 (1)

After a couple of years of trial and error in which I tried to address my autoimmune issues in a holistic way (you can read my story at the bottom of this page), I was able to discover that food intolerances or non-allergic food hypersensitivities were not my only problem. I learned that I also needed to take care of other issues, such as gut dysbiosis, SIBO, intestinal parasites, mold and chemical sensitivity, hormonal imbalances, as well as unmanaged stress and sleep difficulties.

How did I find those other hidden pieces of the puzzle? Well, I looked for the guidance and supervision of professionals who could help me tailor a specific therapeutic approach based on the various (it’s more accurate to say ‘many’) tests and exams that I took throughout the years and that helped me and my functional medicine doctor understand what direction we needed to go.

Did an elimination diet helped me improve my situation? The answer is definitely YES. But would I have had the same results if I ONLY relied on that? Probably not. And what was absolutely crucial was to work with a well-established functional medicine doctor that could accompany me on that journey so that we could investigate other issues.

If you want to give the Autoimmune Protocol (AIP) a try, you can download my COMPLETE AIP FOOD LIST you find below, but if you have done that already and you are not seeing results, maybe it’s time to tackle other potential issues.

The Complete AIP Food List for the Autoimmune Protocol

Enter your email and get the COMPLETE AIP FOOD LIST!

We talk about what to do when elimination diets don’t work with Jennifer Fugo, MS, LDN, CNS, a functional clinical nutritionist with a Master’s in Human Nutrition, who helps people with never-ending ‘stomach problems’, chronic skin rashes, brain fog, chronic fatigue, and autoimmunity find a way to better manage their health symptoms.

Jennifer is also the host of the Healthy Skin Show and the author of the best-selling book The Savvy Gluten-Free Shopper: How to Eat Healthy without Breaking the Bank. But besides all these titles and impressive accomplishments, Jennifer is also a great friend, and because I am lucky to know her in person and I know she has years of experience supporting people with food sensitivities – especially those who are stuck on elimination diets without any improvement – I thought she would be the best person to interview for this post!

What to Do When Elimination Diets Don’t Work. A Talk with Jennifer Fugo 1 (1)

Practical Tips to Use When Elimination Diets Don’t Work:

AMBRA: Jennifer, what is an elimination diet and how does it work?

JENNIFER FUGO: I consider an elimination diet to be any type of diet that requires the removal of food commonly eaten for therapeutic benefit. These types of diets have been commonly employed by nutrition professionals.

The idea is that the elimination diet (when chosen and executed correctly) can improve symptoms and potentially some diagnostic lab markers as well as reduce internally-generated inflammation.

Over the past twenty or so years, elimination diets have grown in popularity thanks to nutrition books because they don’t require a prescription and are typically safe to do on your own for a period of time.

Some “single food” elimination diets (like gluten-free or dairy-free) could be a life-long choice without great concern when you’re eating a nutrient-dense diet.

But more extensive multi-food or food group elimination diets should generally not be used long-term without professional support to avoid some serious health pitfalls.

AMBRA: How does one decide whether they should do an elimination diet or not?

JENNIFER FUGO: Most people decide to do an elimination diet to fix their health. They do an elimination diet either as a “detox” or “cleanse” OR they’re motivated to stop or manage symptoms (ie. diarrhea, gas, bloating, brain fog, eczema, joint pain).

As a clinical nutritionist, I generally look at elimination diets as a test and use the feedback a client will share about their symptom improvement. It can tell you a lot about gut function and their microbiome!

I think doing an elimination diet for 14 to 30 days is generally safe assuming you aren’t already limited on food choices and don’t have a history of eating disorders. Even three or six months may be safe assuming your diet is nutrient-dense and you’re aware of and addressing any hidden nutrient deficiencies.

If you’re pregnant or breastfeeding or have a very complex health situation, this is where getting professional guidance from a nutrition professional with experience in what’s going on is often helpful and at times crucial.

Before doing an elimination diet, it’s best to figure out if you don’t have enough stomach acid which can trigger symptoms that essentially trick you into thinking that you’re sensitive to something. It’s really easy to figure this out by doing a free at-home Low Stomach Acid test that I use in my practice.

What to Do When Elimination Diets Don’t Work

AMBRA: Before embarking on an elimination diet, I tried to look for food sensitivities through blood exams. This strategy seemed much quicker and way less committing, but the results I got were confusing at best. Can you explain why allergy testing is not an accurate tool to discover food sensitivities?

JENNIFER FUGO: You’re not alone! I used to be a big fan of food sensitivity testing (and even paid to have a panel done on myself back in 2008), but generally speaking, I find these panels to be a waste of money (aka. resources).

Allergy testing is different from food sensitivity testing because it’s looking at IgE reactions which can be life threatening! Sensitivity testing looks for IgG reactions.

These reactions can shift and change with exposure to foods meaning that if you’ve already eliminated a particular food, your test could show a false negative.

If I were to do a sensitivity test today, it would likely tell me that I could eat gluten (even though I definitely cannot). The reason is that I’ve been gluten-free since 2008 and so my diet creates a false negative.

Also these results don’t always make sense. One client did an IgG panel on her own only to get results showing a severe reaction to summer squash. She rarely ever ate summer squash and has never had any symptoms to comment on after eating it.

(As an aside, sensitivities are not the same as intolerances. Intolerance reactions result from being missing an enzyme to break something down — ie. diamine oxidase (DAO) breaks down histamine, lactase breaks down lactose).)

Two final points worth making…

  • You cannot determine food sensitivities at all from a hair analysis. That’s a scam.
  • Save your money and consider getting diagnostic testing like a functional stool test used by practitioners such as the GI Map (not Viome which offers very little to no clinical value).
Jennifer Fugo

AMBRA: What can people expect from an elimination diet?

JENNIFER FUGO: This is a great question — and one that often is only promoted based on the benefits. But there are two sides to everything!

If an elimination diet is a good fit given the symptoms someone is experiencing, they may feel more energetic, improved sleep quality, better digestion, less joint pain, less stuffy/runny nose, more clear-headed, better skin health, less inflammation (and may even lose some weight as a result) and may see an improvement in certain lab markers.

This can lead someone to believe that they should just stay on that elimination diet because they want to retain the benefits they’re feeling.

But there are some downsides depending on how restrictive the diet is!

Downsides to staying on an elimination diet (for too long) include:

  • Developing food fear (also known as orthorexia)
  • Nutrient deficiencies
  • Increase in or new symptoms
  • Inability to reintroduce foods due to loss of oral tolerance
  • Gut microbiome shifts NOT in your favor – ie. reduced diversity
  • Decreased social life due to difficulty eating out
When Elimination Diets Don't Work

AMBRA: How long does it take to see results from an elimination diet?

JENNIFER FUGO: Extensive elimination diets should be used for a limited period of time to reduce the potential negative side effects of restricted diet/nutrient diversity. We know from research that the more limited your diet is, the less abundant your gut microbiome will become. 

For example, while helpful for IBS symptoms, a low FODMAP diet will decrease beneficial bacteria that could cause more problems long-term.

The length of time to see or feel results can vary depending on the type of elimination and what’s driving the problem in the first place. 

A gluten-free diet could take anywhere from a week to 6-weeks later to notice a difference whereas the low FODMAP could improve things anywhere from 7-14 days later.

Another example would be the elimination of an IgE food allergy or a food that’s cross-reactive with a pollen allergy. You might feel improvements after a few days!

AMBRA: How long should an elimination diet last and when does it become ‘too long’?

JENNIFER FUGO: Generally, an extensive elimination diet should not be done for longer than 30 to 60 days (maybe 90 if it’s really nutrient dense) without support.

Single food eliminations like gluten or dairy are generally okay to maintain on your own if you find that they aren’t your friend. 

The red flags are when you continue to restrict more and more (thinking that just one more elimination will get your results) or you cannot reintroduce foods after being on a restrictive elimination diet after 30 days

These are signs that there is something else going on under the surface and help from a trained professional would be the best next step.

A general rule of thumb with the low FODMAP diet — if you cannot add FODMAPs back in after a 30-60 day elimination, get help to address gut microbiome issues driving the symptoms. When you rebalance the microbiome appropriately (with more powerful tools than just diet alone), you should be able to reintroduce FODMAPs with relatively little reaction.

Even with AIP — if you do not experience a significant improvement in symptoms after 60 to 90 days max, something else is going on to drive symptoms that you’ll need help with.

What to Do When Elimination Diets Don’t Work

AMBRA: What are the main mistakes people make on an elimination diet?

JENNIFER FUGO: A big mistake is assuming that a pretty severe uptick in symptoms is just normal “detoxing.” If you notice a real uptick in GI symptoms (like diarrhea, bloating, heartburn), get help as that could mean your elimination diet is not mixing well with your gut microbiome.

Also it’s worth pointing out that food sensitivities are not a root cause. The gut must be leaky first in order to develop a sensitivity to food which is why you have to look for issues such as gut dysfunction, medication exposure that increases gut permeability (like NSAID use), gut microbiome dysbiosis + pathogens, and stress to actually figure out what’s driving the food reactions.

Additionally, people will assume that because their elimination diet is nutrient-dense, they couldn’t possibly have any nutrient deficiencies. This comes down to the point that you aren’t what you eat, but you are what you absorb. So if absorption is compromised for whatever reason, you’re likely feeding nutrients to gut bugs and making very expensive poop.

Another very common problem is blaming food for your symptoms and health problems. In some instances like Celiac disease or an IgE allergy, certain foods are a huge piece of the puzzle. But that’s not the case for everyone!

I often tell my clients (and share this advice on my podcast) that it’s not always the food itself causing your symptoms. It’s often what happens to the food once it interacts with your microbiome!

The reality is that dysbiosis (an imbalance of gut flora) and/or the presence of bugs that shouldn’t be there (like H.pylori, Staph aureus, Pseudomonas, Klebsiella pneumoniae, Strep) are the bigger concern. They tend to be the greatest drivers of “leakiness” in your gut… even more than food (including gluten).

These issues are not generally as food-fixable as we’re led to believe which is why elimination diets end up becoming unending symptom management tools. 

And elimination diets have the potential to trigger increased reactivity to eliminated foods which has been discussed more recently by Datis Kharazian

If you find that you cannot add food back in and your diet is getting smaller and smaller, it’s time to get professional help.

Jennifer Fugo

AMBRA: What could be the main reasons why an elimination diet failed?

JENNIFER FUGO: The main reasons that elimination diets fail is often because their hard to maintain in the real world (ie. social situations, traveling, eating out), nutrient deficiencies resulting from limited food choices, and other hidden root causes that diet cannot fix.

In my clinical practice, I assess every client for 16 different root causes that could be driving the health complaints. They include food reactions (like legit IgE food allergies, sensitivities and intolerances), gut dysfunction, gut microbiome imbalance, mitochondrial insufficiency, thyroid imbalances, nutrient deficiencies, toxic exposures, and even drug reactions.

Not all of these issues are food or diet-fixable.

While I’m totally all for Team “Food Is Medicine”, I’ve come to see the damage that’s been done by telling people that food (especially in the form of increasingly restrictive elimination diets) can fix everything. That’s simply not true. 

For example, no diet is going to get rid of H.pylori, a bacteria that hides in the stomach. It’s a pretty common infection worldwide and can deactivate stomach acid increasing your risk of ulcerations and nutrient deficiencies like vitamin B12. Medications and/or botanicals with supplemental nutrients are more effective routes to take.

While it is easy to package a diet within a book, it doesn’t mean it’s the right long-term plan for you especially if your health picture is really complex and you’re pretty sick. Sometimes we need different tools to get us to a point where food then can support and maintain.

Jennifer Fugo Healthy Skin Show

AMBRA: When do you recommend your clients to try an elimination diet? Are certain health or skin issues more likely to benefit from it than others?

JENNIFER FUGO: Unless it’s warranted due to lab testing, I generally don’t recommend elimination diets to my clients. The majority of them have already tried so many of them and may still be stuck on a restricted diet plan due to reactivity or just plain fear.

That said, if you’re eating the Standard American Diet, I would suggest minimizing packaged, processed and refined foods. 90% of the time, I will ask clients to go gluten-free if they aren’t already because gluten has been shown in research to increase gut permeability in everyone. It may not be forever, but at least while we’re working together.

Ultimately my goal is to help someone return to eating as many foods as possible while maintaining good health and quality of life.

AMBRA: I won’t hide that I did encounter some challenges during the elimination period of the Autoimmune Protocol. In particular, I found the reintroduction phase very confusing and I know that many people, after seeing the first improvements, develop a sense of ‘fear’ towards all the foods that they cut out, so much that they end up remaining stuck on a very restrictive diet for many months if not years. Can you tell us something about the side effects of an elimination diet and how to avoid them?

JENNIFER FUGO: One of the best things for you to leave this lengthy article with is that it’s not the food specifically causing the issues. It’s what happens to the food once it gets down into your gut.

Food is not your enemy. But the environment of your GI tract (which includes the actions of digestion, absorption and elimination) can cause you to think that it was the food you just ate that did X to you.

And it makes sense… you eat something, have a reaction and assume that it was the food. But that entire line of thought leaves out the huge, complex gut environment that isn’t so easy to get a clear answer on immediately.

It’s not like we have a tape that will just spit out when you touch your nose that tells you exactly what’s wrong. Diet reactions and other symptoms should be viewed as the way your body communications with you. Admittedly, it’s feedback that’s unfortunately rather vague at times.

So if you’re getting symptoms anywhere in your body after eating certain foods, a better next step would be to question WHY you’re experiencing these symptoms.

Just blaming the food isn’t likely to give you the long-term answers or help that you’re looking for. AND pits you and food (aka. nourishment) against one another.

If you’re stuck on a restrictive diet, I’d suggest making a list of foods you’d like to reintroduce and then working with a practitioner to address root causes so you can start reintroducing foods one at a time.

What to Do When Elimination Diets Don’t Work

AMBRA: I know you used to run the Gluten Free School and that you have loads of experience on gluten related issues. How big a role does removing gluten from your diet play VS going on a full on elimination diet?

JENNIFER FUGO: I recently reviewed a stool panel with a client who had been religiously avoiding gluten for years thinking that it was driving her eczema. Her skin never really improved and she drove herself nuts trying to figure out where hidden gluten was in her diet.

Her stool panel clearly showed us that she had a bunch of very unfriendly bugs (aka. pathogens) in her GI tract and inflammation there as well. She was shocked because she didn’t really have any gut symptoms — it was mostly just skin issues!

This entire time she had been convinced by online doctors that gluten was the issue, but in reality, her gut microbiome is a mess that is causing issues on her skin.

Data like this and working with clients has shifted my perspective on gluten so much that after a certain point, I had to jump off of the “gluten is the devil” train.

While we know that gluten exposure increases gut permeability, it’s not a permanent state of permeability in every person. Some people do retain tolerance to gluten’s effects — though I am not one of them (gluten sensitive but confirmed negative for Celiac). And obviously someone with Celiac would need to religiously avoid gluten for life.

My general rule of thumb is this — if you’re motivated enough by chronic symptoms to want to do something about it (like change your diet), remove gluten.

I’d start with gluten first and see if that will help. Not everyone will experience a change in symptoms, but at the very least, it reduces the level of permeability that’s going on. From there, you could test out other potential foods like dairy or eggs if you feel like you react to them after eating them.

More extensive elimination diets can be tested out, but for a limited period of time and potentially under the guidance of a practitioner if the elimination diet is pretty restrictive.

Jennifer Fugo

AMBRA: If the AIP or other elimination diets don’t work for some people, what do you recommend to them?

JENNIFER FUGO: If AIP or elimination diets aren’t working for you, get help. You aren’t a failure because the diet isn’t getting you the results that others get. You are unique and so is your situation!

Just because someone has the same or similar symptoms (or a health journey) as you doesn’t mean that the root causes driving your problem are the same as theirs.

That’s why you’ve got to look for your combo of root causes so you can take more meaningful and impactful actions.

Look for a nutritionist or dietician with extensive experience looking deeper for root causes driving symptoms who won’t just rely on more elimination diets or a food sensitivity test.

In my virtual clinical practice, I work with clients all over the world with chronic skin rash concerns and those with unending gut challenges who are fed up feeling awful and fearing food. They can’t understand why they have the healthiest diet, but are the sickest person they know. And they have a desire to understand what’s driving their health complaints so they can better support their body.

Yes, elimination diets are powerful tools, but they need to be used wisely. And given the tremendous amount of food fear these days, we all need to think long and hard about how we talk about and use elimination diets.

Because the negative consequences that can result from elimination diets like fearing food aren’t healthy.

Jennifer Fugo

WOW. This was a lot of information. I hope that this great interview with Jennifer Fugo brought you some clarity and helped you answer some of the questions you might have had about what to do when elimination diets don’t work. I receive loads of emails from people who are feeling stuck and hopeless because their elimination diet wasn’t as successful as they had expected… and I hope this talk offered you new perspective and pointed you in the right direction!

Share your experience with elimination diets in a comment below and feel free to ask questions there too!

If you enjoy this interview and think it can help others who aren’t seeing the results they expected from their elimination diet, share it on Facebook, save it on your favorite Pinterest board and subscribe to my weekly newsletter so that you never miss a post!!

Lots of love from Italy and ciao!


What to Do When Elimination Diets Don’t Work. A Talk with Jennifer Fugo
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Ambra Torelli
Born and raised in Italy, Ambra visited over 20 countries and now she divides her time in between Italy and the US, where her husband is from and where she moved in 2011 work as university professor of Italian Literature. She writes about food, travel and things that inspire her! more about ambra

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  • Lisa July 6, 2020 8:45 am

    Thank you! This was very helpful since elimination diets have not worked for me at all. I have a very healthy diet and I AM one of the sickest people I know, also with chronic skin rashes that never get better. Nothing the dermatologists have tried have helped. Thank you again!

    • Jeanine July 6, 2020 1:13 pm

      I suggest trying to look into mast cell disorders.

    • Jennifer Fugo July 6, 2020 5:47 pm

      Hi Lisa, I know how frustrating it can be to feel that way. I was once in your shoes dealing with the exact same thing getting puzzled looks from doctors like I was just making things up. So please — don’t give up. There are answers out there and you have to look for them as I’m guessing you already are since you’re here reading Ambra’s amazing blog!

      I hope that this gives you hope that you won’t be stuck on some tiny diet forever… you just have to get to the root of things and address it from there 🙂

    • ambra July 7, 2020 11:52 pm

      So sorry to hear that Lisa. I really hope that this great interview with Jennifer will help you search alternative ways of healing! <3

  • Anne July 6, 2020 11:34 am

    Great information. I did full elimination for 90 days and have had GI issues almost constantly with reintroductions. I’m now working on possible SIBO with herbs and a low FODMAP diet. I feel like I’m peeling back layers to get to the root cause. Thank you for this valuable info!

    • ambra July 7, 2020 11:49 pm

      Thanks so much for reading Anne! Jennifer is a wealth of knowledge and I knew you guys would have loved to learn from her!

    • Jennifer Fugo July 23, 2020 1:21 pm

      Hi Anne, if you believe you’re dealing with SIBO, I’d recommend checking out my friend Amy over at She’s a dietitian who has personal first-hand experience overcoming SIBO and works with clients who are struggling. Her content is great and she talks a ton about issues with restrictive diets (even the low FODMAP diet) for SIBO. Hope that helps you!

  • Rae July 6, 2020 12:31 pm

    This was fantastic! I’ve never left a comment on a blog before but I felt the need to so with this post. I’ve been to numerous dermatologists an allergist/immunologist and rheumatologist with very little help in trying to address my eczema. I’ve always considered an elimination diet but was overwhelmed by all the different options out there. This was very helpful and has opened my eyes to seeking a nutritionist/dietician that can help. Thank you for sharing!

    • ambra July 7, 2020 11:51 pm

      Rae, wow! Thanks so much for taking the time to write. I am so happy to hear that this post opened your eyes and I hope it’s gonna help you find the answers you are looking for!

    • Jennifer Fugo July 23, 2020 1:26 pm

      Hi Rae, so glad that you happened upon this information! In your process of finding someone, make sure that they specifically understand and work with chronic skin issues. There’s a very small community of practitioners who do. It’s more complicated than just a gut protocol or a histamine issue. Keep that in mind… and that some of us also work virtually and can help you even though we are not in the same city, state or even country. 🙂

  • Annoushka July 8, 2020 12:02 am

    Hi Ambra..I have been diagnosed with hashimotos disease over 17. I suffer with debilitating hives every day…i have tried every single possible diet but it has all failed me. I am interested when u mentioned the root cause being the reason why diets don’twork. How can i find out more about this? Thanks.

    • Jennifer Fugo July 23, 2020 1:24 pm

      Hi Annoushka, Hashimoto’s is often associated with gut issues. The hives could be due to the Hashimoto’s OR they could be due to having a hidden infection (which often can be found from a comprehensive stool test). However if you have a lot of allergies, it could also be a sign of eating IgE cross-reactive foods. Basically something is destabilizing your mast cells. It’s pretty likely that this is all connected, but you’ll likely not get results from diet alone given the complexity of symptoms and issues. Time to look deeper!

  • Denise O. July 13, 2020 8:59 am

    Excellent interview!!! Thank you for the amazing posts you share with us! I’ve been AIP/Paleo for over 5 years with no improvement. I was diagnosed with severe Rheumatoid Arthritis 25 years ago and since then I have been on medications (including Enbrel injections). As I have not had remission in any symptoms (bloating, stomach upset, constipation, brain fog, low energy, fatigue, pain), I’m curious to hear what Jennifer Fugo has to say about the way this disease could be affecting my body in negative way – with food, digestion and absorption. Thank you so much!

    • ambra July 13, 2020 1:13 pm

      Thanks so much for the great feedback Denise! I am so sorry to hear about your struggles. Hopefully you’ll find Jennifer response helpful!

  • XXX June 6, 2022 8:15 am

    Thank you for information. I am struggling on very strict diets (paleo, aip) more than five years to control psoriasis. At first diet helped me a lot, almost cleared my skin, but with the time diet stopped working. Moreover, I have to go on stricter and stricter diet and also developing new food senstivities. In my country there is no such good gut specialists and conventional doctors can only prescribe skin creams with hormones. I know that it is too far for me to come to your office. In this case, could you advise me which blood/stool tests (h-pylori, othe bacterial) should I take in my country doctoral offices? Maybe that could help to identify the cause of my problems. Thank you for your response.

    • Jennifer Fugo August 25, 2022 3:18 am

      Hi there! I’m sorry to hear you’re struggling with this! Depending on the country, you may be able to order the same or a similar stool test that I use with US clients. You could ask your doctor to test for h.pylori, but they generally don’t do other stool testing beyond looking for pathogens. Definitely check out all of the episodes on the Healthy Skin Show podcast about Psoriasis ( and request regular blood work from your doctor (see this list

      And I’ve got a root cause guide here ( that I use with my clients. This will help you know what’s going on for you + where to focus.

      • XXX September 25, 2022 1:13 am

        Thank you for response. I will look more into this. I have recently found that I do not have h-pylori or other fungus in my gut.

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