The autoimmune protocol (AIP) for ulcerative colitis and Crohn’s: does it work?

When you are living with inflammatory bowel disease, whether ulcerative colitis or Crohn’s disease, it is natural to look for dietary solutions. One approach that has gained a lot of attention is the autoimmune protocol diet, sometimes known as the AIP diet.

The autoimmune protocol has been around in different forms for decades. Naturopaths and functional medicine practitioners were recommending elimination diets in the 1980s and 1990s that looked very similar. It was only later that the paleo community helped to popularise AIP online. The diet excludes grains, dairy, beans and pulses, nightshades such as tomatoes, aubergines and peppers, nuts, seeds, eggs and processed foods. The aim is to reduce immune reactivity by cutting out common irritants. While this may sound logical, there is no strong evidence that all of these foods, such as nightshades, need to be avoided in IBD.

What the research says

A small study has suggested that the autoimmune protocol may help people with IBD. While this is encouraging, one study is not enough to prove that it works for everyone. Other dietary approaches have also shown benefits. A low FODMAP diet has been helpful in Crohn’s disease for reducing bloating and abdominal pain. The Mediterranean diet, while less studied specifically in IBD, has strong evidence for lowering inflammation and supporting long-term health. The overall message is that diet does matter, but no single plan is the solution for everyone with colitis or Crohn’s.

Why restrictive diets can mislead

Strict elimination diets such as the autoimmune protocol often promise more than they deliver. Cutting out long lists of foods can bring temporary relief, but it also risks removing many beneficial nutrients unnecessarily. Once foods are reintroduced, symptoms often return. Over the years I have seen many people try strict diets only to feel more anxious and confused about eating, rather than better.

Why diet matters in IBD

A diet that lowers inflammation is vital, but the fastest way to improve is to heal the gut lining so the immune system stops overreacting. At the same time it is important to reduce the body’s inflammatory load through food. That means focusing on an anti-inflammatory way of eating that is different from AIP. Foods that are clearly linked with higher inflammation include sugar, excessive omega 6 fats and saturated fats. For someone with IBD, certain fibres and plant chemicals may also be irritating at first. This is why FODMAP diets can seem helpful early on, although in practice it is better to listen to your own body and use a food diary to identify what genuinely affects you.

Are lectins, phytates and oxalates bad for IBD?

Some of the fears that drive restrictive diets come from concern about compounds such as lectins, phytates and oxalates, sometimes called anti-nutrients. These substances are often blamed for harming the gut, yet the evidence does not support this view. Cooking, soaking and sprouting greatly reduce their levels, and when eaten as part of a balanced diet they are not harmful. In fact, populations that eat plenty of beans, wholegrains, nuts and leafy greens, all of which contain these compounds, consistently show better health outcomes and longer life expectancy. For people with colitis and Crohn’s the real danger is not these compounds but cutting out too many plant foods, because this reduces fibre intake, microbiome diversity and the production of short-chain fatty acids such as butyrate. These are all central to gut healing.

Why trends like the carnivore diet are concerning

Another trend that has become popular online is the carnivore diet. At first it can look as if it helps, because by removing all plant foods it also removes many of the common irritants and fibres that may trigger symptoms in the short term. But this is not the same as healing. The idea that all plants are toxic and inflammatory is simply wrong. Research shows that plants do the opposite. They support the gut by encouraging the production of protective mucus, they feed the colonic cells known as the epithelium through short-chain fatty acids like butyrate, and they nourish the microbiome. A diverse microbiome produces healing substances and crowds out harmful bacteria.

There is also evidence that diets high in red and processed meat are associated with worse flares in IBD. A meat-heavy diet raises saturated fats and omega 6 fats, both of which are linked with higher inflammation. In addition, animal protein and fat can encourage the production of compounds such as trimethylamine-N-oxide (TMAO), associated with inflammation and cardiovascular risk. This makes the carnivore approach risky in the long term.

That does not mean protein itself is harmful. On the contrary, protein is vital for repairing tissues and rebuilding strength. After a flare the body’s requirement for protein is significantly higher, because healing the gut lining, restoring muscle mass and supporting the immune system all depend on it. The key is to include protein as part of a balanced anti-inflammatory diet that also contains plant foods, rather than taking it to extremes that cut them out.

A three-phase plan for colitis and Crohn’s

In my 26 years of working with people with ulcerative colitis and Crohn’s I have studied every diet in detail. I have looked at the research, seen what works in practice, and developed a method that goes further than a one-size-fits-all elimination diet. My approach is built around three phases.

In the first phase the diet is low in irritants and low residue. It avoids common intolerances and focuses on soothing the gut. The second phase restores balance to the microbiome, increases anti-inflammatory nutrients and supports the gut lining in producing more protective mucus. The third phase focuses on healing the lining of the gut, addressing leaky gut, and carefully working through food intolerances. These often reduce as healing progresses, but people need guidance and reassurance while that happens.

Why mind-body support matters

Ulcerative colitis and Crohn’s are not just physical illnesses. Stress, anxiety, poor sleep and worry about flares all affect the gut directly. That is why I include gut-directed hypnotherapy, mindfulness approaches such as ACT, breathwork and Emotional Freedom Techniques. These calm the nervous system and in turn help to calm the digestive system. They also provide essential psychological support, which is vital because healing is rarely straightforward. It is usually a zigzag, with progress, setbacks and doubts along the way. Having support and a clear path makes a huge difference.

Final thoughts

So is the autoimmune protocol the answer for IBD? It might bring some relief, but the evidence is limited and the diet is highly restrictive. The real path to long-term stability is broader. It involves lowering irritants, restoring the microbiome, healing the gut lining and supporting the mind and body together. That is exactly what I cover in my book and course. If you would like to discover a structured three-phase plan designed for people with colitis and Crohn’s, join my mailing list to be the first to know when they are released.