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Your 3-Step Microscopic Colitis Diet Guide

Key Takeaways:

If you’re dealing with ongoing watery diarrhea, belly pain, weight loss, and feeling very tired, a microscopic colitis diet may help relieve your symptoms. There’s no one perfect plan, but a simple step-by-step approach may help you find which foods trigger symptoms and which support healing.

Microscopic colitis (MC) is a type of inflammatory bowel disease that can significantly disrupt your life with chronic, watery (non-bloody) diarrhea, abdominal pain, weight loss, and fatigue. 

The exact cause of MC is unclear, but smoking and certain medications may raise the risk. Because research is still limited, treatment options are few. Doctors usually recommend quitting smoking and stopping certain medications, which might help some people but may not fully address the root causes. 

In our clinic, we focus on giving people tools to manage their total digestive health. We know MC is linked to long-term inflammation, a dysregulated immune system, and problems with gut microbes 1. Fortunately, simple (though not always easy) changes can help restore gut health and reduce symptoms. 

I’ve found that changing the diet is the most effective way to improve gut health and overall well-being, so that’s where I start. There’s no single diet that works for everyone with MC, but options like Paleo, low FODMAP, and the Autoimmune Protocol can help correct any poor gut health that’s contributing to it. 

In this article, I’ll explain the process we use in the clinic to find the best diet for each client. Since microscopic colitis isn’t well known, I’ll start with some background before diving into the diet details.

Microscopic Colitis 101

Microscopic colitis (MC) is a lesser known type of inflammatory bowel disease (IBD) that affects the colon’s lining. It’s thought to be related to autoimmunity and most often appears as one of two types 2:

  1. Lymphocytic colitis: LC means more lymphocytes (white blood cells, a type of immune system cell) are in the colon lining.
  2. Collagenous colitis: CC means a thick layer of collagen (a type of protein) is in the colon lining.

Microscopic colitis can be missed or mistaken for something like IBS because during a colonoscopy the colon often looks normal—unlike in other types of IBD like Crohn’s disease and ulcerative colitis 3

Microscopic colitis is considered a type of IBD, but it’s not the same as Crohn’s or ulcerative colitis. It doesn’t raise your risk of strictures, fistulas, or colon cancer, and it usually causes less severe symptoms 4. It’s also harder to diagnose.

To diagnose microscopic colitis accurately, your doctor needs to go beyond a regular colonoscopy and take a small tissue sample from your colon. They will then look at the sample under a microscope to spot signs of the condition.

MC can significantly impact your quality of life and, if left untreated, can lead to nutritional deficiencies and dehydration 2. The most common symptoms of microscopic colitis can include 5:

  • Frequent, watery diarrhea without blood (can happen up to 15 times a day)
  • Sudden, urgent need to use the bathroom, sometimes during the night
  • Trouble controlling bowel movements (accidents)
  • Belly pain
  • Belly cramps
  • Achy joints
  • Losing weight without trying
  • Feeling very tired or worn out

These symptoms can come and go and often look like other gastrointestinal conditions. That and the fact that the diagnostic process is more involved can make it hard to get a clear diagnosis. 

What Causes Microscopic Colitis?

Though it’s not yet known if there’s one specific cause, microscopic colitis seems related to both genetic factors and environmental triggers. These risk factors increase the likelihood that you’ll develop MC 3:

  • Having an autoimmune condition, especially celiac disease, but also conditions like type 1 diabetes, rheumatoid arthritis, or Hashimoto’s thyroiditis
  • Smoking 
  • Using certain commonly prescribed medications like proton pump inhibitors (PPIs), selective serotonin reuptake inhibitors (SSRIs), and non-steroidal anti-inflammatory drugs (NSAIDs)
  • Having a previous gastrointestinal infection
  • Bile acid malabsorption, a digestive disease where bile acids build up and cause diarrhea

Most of these risk factors speak to the importance of gut health on microscopic colitis.

If you develop MC as the result of a medication or smoking, simply removing that drug or quitting smoking might be enough to stop the disease process. However, if you continue to struggle, you’ll need to look at other treatments that target other probable root causes of the disease—like gut health and autoimmunity. 

Since there’s a shortage of research on microscopic colitis, there are no FDA-approved medications for it yet. Most healthcare providers prescribe drugs designed to treat Crohn’s disease or ulcerative colitis—but these may not work well for MC 6

So, what can you do to heal? In the clinic, we’ve found that targeting gut health and immune health with a microscopic colitis diet can get most people feeling well again.

Microscopic Colitis Diet: A Step-By-Step Guide 

Just because we don’t fully know what causes microscopic colitis, it doesn’t mean your symptoms can’t get better. Like other bowel diseases, MC seems to occur when the gut is imbalanced and the immune system is overreacting and causing too much inflammation. The good news is we can work on these problems by changing what you eat.

I wish there was one obvious diet for MC, but there isn’t. In the clinic, we use a step-by-step approach to find the best diet for each person. As I explain in Healthy Gut, Healthy You, we usually start with a gut reset to help calm the immune system and reduce inflammation.

Step 1: Gut Reset

In this first step, we’re essentially hitting the reset button to achieve quick symptom relief. In the clinic, I typically recommend starting with a gut reset. This is a type of fasting that involves replacing all normal meals with an elemental diet shake (we use Elemental Heal) for 1–3 or up to 4 days. If you’ve never done this type of fasting, it may sound daunting. But this process can provide tremendous relief. 

Elemental diets can help the gut rest from normal digestion, which supports healing by lowering inflammation 7, aiding tissue repair 8, and cutting off food sources for bacterial or fungal overgrowths 9. Because the elemental formula is absorbed in the upper part of the small intestine, the rest of the digestive tract gets a chance to rest and recover.

We find that at least 2 days on an elemental diet tends to benefit people with MC the most. We tell our clients: If things are going well at the end of day 2—your symptoms are better and your energy is good—it’s usually safe to continue for another day or two if you wish. But if there’s no desire to continue after the second day, it’s fine to stop then. 

If severe symptoms arise on any day, it could mean you’re allergic to something in the formula. Stop the elemental diet and contact your healthcare provider. If an elemental diet doesn’t work, check out alternative options in my free Gut Reset Guide.

After finishing the gut reset, our next step is to figure out which diet works best for managing microscopic colitis. There are several diets to choose from, but you don’t have to jump to the strictest one right away. I recommend starting with the least restrictive option and only tightening it up if necessary. 

Step 2: Diet Reboot

Since we’re working to rebalance the gut, reduce the immune system’s burden, and lower inflammation levels, we need a diet that’s low in common allergens and unlikely to cause food intolerances. This kind of elimination diet will also replace ultra-processed foods with whole and minimally processed foods without added sugar. 

We typically start with the broadest anti-inflammatory diet—Paleo—and move on to more restrictive diets if symptoms don’t improve. 

Start With Paleo 

A Paleo diet can help reduce inflammation by cutting out foods that trigger the immune system 10 11, and studies show it can lower inflammation markers like CRP 12 13 14

A Paleo diet may also help improve symptoms in people with IBD 15

On a Paleo diet, you’ll focus on eating whole or minimally processed:

  • Vegetables and fruits
  • Meats, fish, and eggs
  • Healthy fats and oils
  • Nuts and seeds

You’ll avoid:

  • Grains
  • Beans and legumes
  • Processed foods
  • Dairy
Your 3-Step Microscopic Colitis Diet Guide - Paleo%20diet%20food%20list L

For my clients, I recommend:

  • Follow a Paleo diet for at least 2 weeks and then re-evaluate how you feel. 
  • If you’re feeling great, keep eating a Paleo diet until your symptoms have mostly cleared up and you’ve reached your best level of improvement. 
  • Then, move onto step 3 and begin reintroducing some of the healthy whole foods you’ve eliminated—this will help you determine your tolerance and personalize your diet.
  • However, if you don’t feel much better after a couple weeks, try a low FODMAP diet.

Not Better? Try Low FODMAP

If the Paleo diet doesn’t improve symptoms, the next step we recommend for our MC clients is a low FODMAP diet

Bacterial overgrowth is more common in other types of IBD and may contribute to microscopic colitis as well 1 16. A low FODMAP diet can help by starving overgrown bacteria, reducing their numbers, and easing digestive symptoms. 

FODMAPs—fermentable oligosaccharides, disaccharides, monosaccharides, and polyols—are hard-to-digest carbohydrates that can feed gut bacteria and be poorly absorbed. They’re high in certain foods, such as broccoli, onions, apples, pears, beans, cashews, wheat, and milk. By limiting FODMAPs, the diet addresses both bacterial overgrowth and carbohydrate malabsorption. 

When there are too many bacteria in the gut, undigested carbs can lead to gas, bloating, and diarrhea 17. Studies show that a low FODMAP diet can reduce IBD symptoms 18 and IBS symptoms 19.

Here’s a brief list of what to eat on a whole-foods, low FODMAP diet:

Your 3-Step Microscopic Colitis Diet Guide - Low%20Fodmap%20diet%20food%20list L

To find out what to avoid and how to combine low FODMAP with other diets, download our free Low FODMAP Guide. Monash University also has a handy app that can help you tailor a healthy low FODMAP diet. 

Just like with the Paleo diet, we advise our clients to follow a low FODMAP diet for at least two weeks, guiding them as follows:

  • If you’re feeling better after week two, you can follow this diet for up to six weeks, or until you regularly have only mild symptoms or none at all. It’s safe to eat this way for at least 6 months IF you follow advice from a Registered Dietician Nutritionist (RDN) on how to cover your nutritional needs and avoid disordered eating 20.
  • For most people, about a month is the sweet spot—long enough to see the most symptom relief without being overly restrictive.
  • The goal isn’t to stay on a low FODMAP diet forever—it’s to heal your gut so you can enjoy a wide variety of healthy foods without symptoms. Most people can reintroduce many eliminated foods without problems, so don’t hesitate to begin reintroducing them as part of step 3.
  • However, if you’ve already tried both Paleo and low FODMAP diets for the recommended time and still have daily symptoms, it might be time to try the Autoimmune Protocol (AIP) diet.

Still Struggling? Try AIP

Your 3-Step Microscopic Colitis Diet Guide - Autoimmune%20Protocol%20food%20list L

When our clients respond partially to the Paleo and low FODMAP diets, we’ll often try the Autoimmune Protocol Diet. The AIP is a more strict version of the Paleo diet and eliminates the following:

  • All grains (like wheat, rice, oats, corn, etc.)
  • Eggs
  • All dairy products, including ghee, kefir, milk, cheese, and cream
  • All legumes, such as green beans, black beans, white beans, peanuts, kidney beans, and chickpeas
  • Nightshade vegetables—like tomatoes, potatoes, peppers, eggplant, and tomatillos—and spices made from them (like paprika and cayenne pepper)
  • All nuts and seeds, such as almonds, walnuts, and chia seeds, along with anything made from them (like seed oils, vegetable oils, or almond flour)
  • Spices made from seeds, like fennel, cumin, dill, anise, mustard, coriander, and nutmeg
  • Alcohol and coffee
  • Added sugars, artificial sweeteners, and food additives

As you can see, the AIP diet is very restrictive, so I only recommend it for MC clients who haven’t felt significantly better on the other less restrictive diets. 

Early research suggests the autoimmune protocol (AIP) diet may help people with Crohn’s disease or ulcerative colitis by reducing symptoms 21 and improving quality of life 22. The diet may also reduce inflammation 21, though not all inflammation markers consistently improve 23.

The good news is you don’t have to follow the diet perfectly to see results. Sticking with it for a couple weeks is a solid start. If it feels too hard, try cutting out just a few of the restricted foods for a week or two and see how your body reacts—then continue working through the rest at your own pace.

Microscopic Colitis Diet Summary

The Paleo diet cuts out many allergens and inflammatory foods, a low FODMAP diet targets bacterial overgrowths, and the AIP diet removes even more allergens. These diets build on each other, so it’s important to take it step by step.

Give each diet 2–3 weeks to see if it helps. If not, try the next more restrictive one. Don’t stress about being perfect—doing your best is enough. The goal is to find what works best for you. Next, we’ll cover how to safely reintroduce foods and find your right diet.

Step 3: Personalize Your Diet 

Once MC symptoms have improved a lot, it’s time to start adding back healthy whole foods. How long this takes may depend on how bad the flared MC symptoms were. Typically in the clinic, it can take anywhere from a couple weeks to a few months. 

It’s important to remember that elimination diets are temporary—not about avoiding your favorite foods forever. You don’t have to be perfect—if you really want a certain food, try adding it back and see how you feel.

Here’s a look at the food reintroduction process we coach our clients through:

  1. Develop a baseline idea of how you feel before reintroducing foods to help you clearly see how your body reacts. 
  2. There’s no hard-and-fast rule about what to reintroduce first—whole and nutrient-dense foods are ideal, and start with whichever of these you miss the most.
  3. Add back one food at a time so you can figure out which ones cause problems. If you try several foods at once and have a reaction, it’s harder to know which food is the cause.
  4. Eat the food you’re testing several times a day for a few days. Most food reactions aren’t all-or-nothing—you might handle small amounts okay, so trying a few servings helps find your limit.
  5. If a food causes symptoms, avoid it for now and try again later. 

If the reintroduction period feels overwhelming and you want a little more structure to your reintroduction process, that’s completely normal. Many people feel this way during this phase. 

I’ve put together a table showing food groups and example foods you may want to try first, and what kinds of symptoms to look for in the process. This is a methodical process that can take time, but reintroducing foods in a clear, structured order can help you identify which ones you tolerate and which may still cause symptoms. 

Food Group Example Foods Common Symptoms to Look For
Dairy (lactose-free first) Yogurt, hard cheese, ghee
  • Digestive issues (bloating, gas, diarrhea, constipation)
  • Skin reactions (rashes, acne, itching)
  • Fatigue or brain fog
  • Joint pain or muscle aches
  • Headaches or migraines
  • Mood changes (anxiety, irritability, depression)
Grains (gluten-free first) Rice, oats, quinoa
Legumes Lentils, chickpeas
Nightshades Tomatoes, potatoes, peppers
Eggs Whole eggs, egg yolks, egg whites
Nuts & Seeds Almonds, sunflower seeds
Gluten (if reintroducing) Whole wheat, barley, spelt

Diet changes are important and can relieve MC symptoms for some people, but they may not be enough for everyone. Fortunately, other natural treatments can help, too. In the clinic, we use a 4-step process for many MC clients—including a gut reset, diet and lifestyle changes, probiotics, and antimicrobials, which I’ve outlined for you in this article.

Find Your Personal Microscopic Colitis Diet

Microscopic colitis can be challenging, but what you eat can offer real relief by addressing the likely root causes: inflammation, an overreactive immune system, and imbalanced gut microbes. 

There’s no one-size-fits-all diet when you have MC, but following a step-by-step approach—starting with an elemental reset and progressing through Paleo, low FODMAP, or AIP—can help you feel better. Once your symptoms improve, you can personalize your diet by reintroducing healthy foods gradually and adjusting as needed, according to what your body tells you. 

If you need more support—like diet and lifestyle protocols and a guide to probiotics—for MC flares, consider working with us directly at the Ruscio Institute for Functional Health.

The Ruscio Institute has developed a range of high-quality formulations to help our clients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you. The information on DrRuscio.com is for educational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.

➕ References

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