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Microscopic Colitis Diet: Finding What Works for You

A 5-Step Process for Determining Your Ideal Microscopic Colitis Diet

Key Takeaways:

  • Microscopic colitis is a type of inflammatory bowel disease that causes chronic, watery, non-bloody diarrhea.
  • Traditional treatments like smoking cessation and medications don’t often treat the underlying causes of microscopic colitis, like inflammation, a dysregulated immune system, and microbial imbalances.
  • Natural therapies like diet, probiotics, and antimicrobials can effectively treat the root causes of microscopic colitis.
  • There’s no specific microscopic colitis diet—rather, there is a spectrum of choices, including Paleo, low FODMAP, and Autoimmune Protocol.
  • Working through our step-by-step process will help you determine which microscopic colitis diet works best for you.

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. Research hasn’t pinpointed one specific cause of MC, but smoking and certain medications (like proton pump inhibitors) seem to increase the risk. Since the research into MC is still in its infancy, we don’t have a lot of solid solutions yet for treating it. Your doctor will probably recommend smoking cessation (if this applies to you) and removing offending medications. While these strategies may be effective in the short term, they may not fully address the root causes of microscopic colitis. 

Our goal in the clinic is to empower you with the tools you need to take control of your digestive health. We may not yet have all the answers about MC, but we do know that it’s rooted in chronic inflammation, immune system dysregulation, and microbial imbalances. The powerful message here is we can target all of these contributing factors with natural solutions like diet, lifestyle, probiotics, and antimicrobials to restore robust gut health and help you finally get off the symptom merry-go-round. 

In my clinical experience, diet is the most impactful intervention for improving your gut and overall health, so that’s usually the first place I start. There isn’t a perfect microscopic colitis diet, rather we have a spectrum of choices (like Paleo, low FODMAP, and Autoimmune Protocol). In this article, I’ll walk you through the process we use in the clinic to determine your ideal diet for MC. Since microscopic colitis is mostly unknown, I’ll give you some background information before getting into the specifics of diet.

Microscopic Colitis 101:

Microscopic colitis (MC) is a less well-known type of inflammatory bowel disease (IBD) that affects the colon’s lining. It most often presents as one of two subtypes [1]:

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

Microscopic colitis may be overlooked as a cause of your symptoms or misdiagnosed as another condition (like IBS) because your colon tissue tends to look normal during a colonoscopy (a test used to diagnose other forms of IBD like Crohn’s disease and ulcerative colitis) [2]. Getting an accurate MC diagnosis requires your gastroenterologist to take it a step further by collecting a tissue sample (biopsy) of the lining of your colon (large intestine) and then viewing those epithelial cells under a microscope. 

MC can significantly impact your quality of life and, if left untreated, can lead to nutritional deficiencies and dehydration [1]. The most common symptoms of microscopic colitis can include [3]:

  • Chronic, watery, non-bloody diarrhea (up to 15 times a day)
  • Bowel movement urgency, often at night
  • Fecal incontinence (inability to control bowel movements)
  • Abdominal pain
  • Abdominal cramping
  • Joint pain
  • Weight loss
  • Fatigue

These symptoms can come and go and often mimic other gastrointestinal conditions. Coupling this with the need for a colonoscopy and histology (viewing cells under the microscope), you’re probably developing a better picture of why getting an accurate diagnosis can be so tricky. So, what causes microscopic colitis in the first place? 

What Causes Microscopic Colitis?

While it’s not yet known if there’s one specific cause, microscopic colitis seems to be the result of both genetic factors and environmental triggers. There are certain risk factors that increase the likelihood that you’ll develop MC [2]:

  • 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

If you develop MC as the result of medication use or smoking, simply removing that pharmaceutical or smoking cessation may be enough to stop the disease process temporarily. 

However, if you continue to struggle, you’re often left with treatments that mask symptoms rather than target the root causes of the disease. Since the research into microscopic colitis is lacking, there are no FDA-approved medications at this time. Most healthcare providers prescribe drugs designed to treat Crohn’s disease or ulcerative colitis, which may not work well for MC [4]. So, what, if anything, can you do to foster healing? This is where targeting root causes with a microscopic colitis diet can be extremely impactful.

Microscopic Colitis Diet: A Step-By-Step Guide 

We may not fully understand what causes microscopic colitis, but that doesn’t mean we can’t reverse the severity of your symptoms. Like other inflammatory bowel conditions, MC is characterized by an inappropriate immune system response and out-of-control inflammation. The great news here is we can target these underlying causes with natural therapies like diet.

I wish I could tell you there’s one specific diet for MC, but that’s just not the case. So, instead of recommending a single dietary plan, we use a step-by-step process in the clinic to help you determine which diet is best for you. As I discuss in Healthy Gut, Healthy You, I like to start with an elemental gut reset to help calm your immune system and inflammation.

Step 1: Elemental Diet Reset

In this first step, we’re essentially hitting the reset button to help you find quick symptom relief. Digesting and absorbing nutrients is a complicated process for your digestive system. The elemental diet is a hypoallergenic, anti-bacterial, anti-inflammatory meal replacement shake that takes the pressure off your digestive tract, giving it a chance to rest and heal. Elemental diets have long been prescribed for other kinds of IBD because they reduce inflammation, reverse the underlying causes of autoimmunity, and prevent flare-ups [5, 6, 7].

For our purposes, I recommend starting with a 2–4 day “fast” where you replace solid foods with Elemental Heal. If you’ve never done this type of fasting, it may sound daunting. But in my experience in the clinic (and personally), this process can provide tremendous relief. So, start with the goal of 2 days on the elemental diet since that’s probably the timeframe where you’ll experience significant improvement. If things are going well, then you may want to continue on for the full 4 days. Of course, some people have trouble with fasting. So, if you’re not feeling it after the second day, then stop at day 2. 

Once you’ve completed your elemental diet reset, it’s time to determine which microscopic colitis diet will be most effective for you. While there are many dietary plans out there, you don’t need to start with the most restrictive one first. I’m a proponent of using the least restrictive option initially and only restricting further if needed. With that in mind, let’s review the Paleo diet as a great starting point for step 2. 

Step 2: The Paleo Diet

Since we’re working to reduce your immune system burden and lower your inflammation levels, we need a diet that’s low in common allergens and food intolerances, as well as ultra-processed foods and sugar. The Paleo diet helps to calm inflammation by minimizing your exposure to foods that provoke an immune response [8, 9] and has been found to decrease inflammation markers (like CRP) [10, 11, 12]. Additionally, the Paleo diet may have clinical benefits for IBD [13]. 

On the Paleo diet, you’ll focus on eating:

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

You’ll avoid:

  • Grains
  • Beans and legumes
  • Processed foods
  • Dairy

I recommend following the Paleo diet for at least 2 weeks and then re-evaluating how you feel. If you’re feeling great, then continue on with the Paleo diet until you’ve reached maximum benefit. At that point, you can move on to step 5 and begin reintroducing some of the whole foods you’ve eliminated to determine your tolerance. 

However, if you don’t feel much better, move on to step 3 and try a low FODMAP diet.

Step 3: Low FODMAP Diet

If you try the Paleo diet and don’t improve as much as you’d like, a low FODMAP diet is the next step. Bacterial overgrowths are more common in people with IBD, so it’s possible that they may be contributing to your microscopic colitis symptoms, too [14, 15]. A low FODMAP diet helps to starve bacteria in the small intestine, which reduces their numbers and relieves digestive symptoms in the process. 

FODMAP stands for fermentable oligosaccharides, disaccharides, monosaccharides, and polyols. These are mainly carbohydrates that feed bacteria or can be difficult to digest. So, in addition to starving bacteria, we’re also addressing carbohydrate malabsorption with a low FODMAP diet. 

Carbohydrate malabsorption is tied to bacterial overgrowths. Your gut bugs are responsible for digesting the fibrous parts of carbohydrates. When everything is working like it should, you don’t notice this process. But if you have too much bacteria in your gut, eating too many of these types of carbs may contribute to symptoms like gas, bloating, and diarrhea [16]. A low FODMAP diet has been found to improve diarrhea in people with IBS [17], improve IBS symptoms in patients with IBD [18, 19, 20, 21], as well as reduce leaky gut and inflammation [22, 23].

Here’s an overview of a low FODMAP diet:

Microscopic Colitis Diet: Finding What Works for You - Low%20Fodmap%20diet%20food%20list L

This is just a brief overview. Monash University has a very handy app that goes into much more detail about a low FODMAP diet. 

Just like with the Paleo diet, it’s best to follow a low FODMAP diet for at least two weeks. If you’re feeling much better, you can stick with this diet for up to three months. However, a month seems to be the most common duration for peak symptom relief and minimal restriction. Rather than continuing a low FODMAP diet for infinity, the goal is to heal your gut so you can eat all of these foods with no negative reactions. In the clinic, many patients are able to reintroduce the majority of eliminated foods with no issues, so don’t be afraid to start the food reintroduction process outlined in step 5.

If you’ve tried both Paleo and low FODMAP for the timeframes suggested but still have lingering symptoms, you may want to move on to step 4 and try the Autoimmune Protocol Diet (AIP).

Step 4: The Autoimmune Protocol Diet


If you’ve only partially responded to the Paleo and low FODMAP diets, the Autoimmune Protocol Diet (AIP) may be an option. The AIP is a more strict version of the Paleo diet. Here’s a list of foods to avoid:

  • All grains
  • Eggs
  • All dairy products, including ghee, kefir, milk, cheese, and cream
  • All legumes, such as green beans, black beans, white beans, kidney beans, and garbanzo beans
  • Nightshade vegetables, including tomatoes, potatoes, peppers, eggplant, tomatillos, and spices derived from nightshades, like paprika, and cayenne pepper
  • All nuts and seeds, such as almonds, walnuts, and chia seeds, including their derivatives, like seed oils and vegetable oils (for example, canola oil, walnut oil, or almond flour)
  • Spices derived from seeds, including fennel, cumin, dill, anise, mustard, coriander, and nutmeg
  • Alcohol and coffee
  • Added or artificial sweeteners and food additives

As you can see, the AIP diet is extremely restrictive, so I only recommend it if you’ve not experienced significant improvement with the other less restrictive diets. But there is a time and place for the AIP diet for some. Patients with IBD who followed an AIP diet for 11 weeks experienced improved quality of life [24] and IBD scores, and some patients had signs of mucosal (the lining of the intestine) healing [25]. In addition, a small study found the AIP diet to reduce IBD disease activity [26].

It’s worthwhile to know that you may not need to follow the diet perfectly to reap the benefits. If you can follow the AIP diet for a couple of weeks to see how your body responds, then great. If it feels way too challenging, you may want to try eliminating a couple of the foods for one or two weeks and see how your body responds until you’ve worked your way through the list. 

To summarize, the Paleo diet removes allergens and inflammatory foods, a low FODMAP diet helps to starve bacterial overgrowth, and the AIP diet further restricts allergens. This process may seem like a lot, but these diets are progressions of one another, and they naturally build upon each other, so take it one step at a time.

Remember, it only takes 2–3 weeks to evaluate whether a diet is working for you. If it’s not, then move on to the next option. Additionally, if strict diets stress you out, it can derail your healing process. Just do the best you can, and don’t beat yourself up if you can’t follow a diet perfectly. This entire process is designed to help you determine what works best for your body. So, let’s get into how you reintroduce eliminated foods when you’re ready to enjoy your new food freedom.

Step 5: Food Reintroduction

Once you’ve reached pretty significant symptom improvement, it’s time to reintroduce eliminated foods. The timeframe on this will likely depend on how severe your symptoms were to start with, and could be as little as 2 weeks to a few months. 

It’s probably best to at least have symptom stability before adding eliminated foods back in so you can get a good sense of how your body responds to certain foods. Having said that, the timing of your food reintroduction also depends on where you are mentally—following a restrictive diet can feel daunting and isolating, especially with regard to social situations. It’s helpful to remind yourself that an elimination diet is temporary, so you won’t be avoiding your favorite foods forever. And you don’t have to be perfect. If you’re really missing a certain food, add it back and see how you feel. Here’s a look at the food reintroduction process:

  1. There’s no hard and fast rule about what to reintroduce first, but you’ll likely want to start with whatever feels the most restrictive to your diet or the foods you miss most.
  2. Try to reintroduce one food at a time. This helps to isolate which foods are problematic for you. If you add back several foods at the same time and have a negative reaction, you’ll have a more difficult time pinpointing the culprit.
  3. Try several servings of the food you’re reintroducing daily for a few days. Outside of food allergies, it’s rarely all or nothing with food. You may tolerate a small amount, so having a few servings will help you identify if you have a certain threshold.
  4. Continue to avoid foods you react to and then try to reintroduce them at a later time. 

I want to point out that while dietary changes are very important and can be extremely impactful, they’re not the only option for healing your MC symptoms, and they may not lead to complete resolution on their own. In the clinic, we use a 4-step process that includes the elemental reset, diet and lifestyle changes, probiotics, and antimicrobials, which I’ve outlined for you in this article.

Personalizing Your Microscopic Colitis Diet is the Key

Microscopic colitis is a type of inflammatory bowel disease that can wreak havoc on your quality of life and overall health. Traditional treatments include removing potential triggers like smoking and certain medications. These options can provide some relief but don’t often address the underlying causes of microscopic colitis. While the research into MC is limited at this time, we know that inflammation, altered immune system function, and microbial overgrowths are common. Natural treatments like diet, lifestyle, probiotics, and antimicrobials are very effective at targeting the underlying causes of MC. 

There’s no specific dietary plan for microscopic colitis. Still, you may want to start with an elemental diet reset and then work your way through our step-by-step process for determining the best microscopic colitis diet for you. The Paleo diet is a great first option, as it removes potential allergens and foods that may cause inflammation. If you don’t experience complete symptom resolution, move on to a low FODMAP diet to help starve bacterial overgrowth. If Paleo or low FODMAP don’t lead to significant improvement, then you can try the more restrictive Autoimmune Protocol Diet to restrict allergens further. 

Once you’ve found the most effective microscopic colitis diet for you, follow it until your symptoms are mostly resolved and then begin reintroducing eliminated foods to determine your tolerance. None of these diets are meant to be followed long-term. If you go through the step-by-step process and find you’re still struggling with microscopic colitis symptoms, you may want to complete our entire 4-step process for healing MC or work with us directly at the Ruscio Institute for Functional Health. 

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➕ References
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