AIP Modifications for IBD Flare

Let’s be real flare ups of Inflammatory Bowel Disease (IBD) are the actual worst. You’re suddenly forced to stay within running distance to your toilet, see scary symptoms like blood and mucus, and often experience painful cramping, loss of sleep, weight loss, dehydration… You get the picture.  While the elimination-phase of the Autoimmune Protocol can be a wonderful tool for decreasing systemic inflammation and improving autoimmune symptoms, sometimes modifications to the protocol are necessary for IBD flares. 

Fats & Proteins

Certain fats and proteins can be more difficult to digest than others, so it is important to focus on lean cuts of cut meat, seafood, and organ meats as well as monounsaturated fats as opposed to saturated fats during a flare up of symptoms.

Foods to Avoid:

  • Fat-rich meats (lamb, poultry with skin, ground beef, pork)
  • Bacon & Sausage
  • Animal Fats (lard, tallow, duck fat)

Foods to Include:

  • Lean proteins (chicken or turkey breast, fish & seafood, organ meats)
  • Olive oil, avocado oil
  • Coconut oil (in moderate amounts)
  • Olives, avocados


High fiber vegetables can trigger more frequent bathroom trips while in the midst of an IBD flare. High FODMAP vegetables can also cause trouble because the sugars aren’t fully absorbed during digestion and can be irritating to the intestines during flares. It is best to focus on well-cooked and low-FODMAP veggies. 

Foods to Avoid:

  • All raw vegetables
  • High FODMAP vegetables 
  • High amounts of any vegetables at one time (aim for ½ to 1 cup per meal)

Foods to Include:

  • Low FODMAP vegetables
  • Well-cooked vegetables


Similar to vegetables, the natural sugar and fiber content in fruit can make IBD flare symptoms worse. It is best to avoid high FODMAP fruits and concentrated forms of fruit juices and focus on low fiber/ low FODMAP fruits instead.

Foods to Avoid:

  • High fiber fruit (berries, mango, oranges)
  • High FODMAP fruits
  • All dried fruit & fruit juices
  • Fruit smoothies
  • High amounts of fruit (aim to ½ cup per day)

Foods to Include:

  • Low FODMAP fruits
  • Low fiber fresh fruits without skins or seed (applesauce, peeled peaches)


Again, it is important to moderate fiber intake when it comes to choosing AIP-friendly vegetables during an IBD flare, as the excess starch and fiber can be difficult to digest. 

Foods to Avoid:

  • High amounts of all starchy vegetables (aim for 1 – 1.5 cups per day)
  • Sweet potatoes with skin on
  • High amounts of squash (due to fiber)

Foods to Include:

  • Moderate portions of sweet potato without the skin, winter squash, parsnips, rutabaga, plantains, etc. 


It is really best to avoid all sweeteners during an IBD flare as the excess sugar can exacerbate inflammation symptoms in the gut and trigger more frequent bathroom trips. 

Other Things to Consider

  1. Make sure you are drinking plenty of water and hydrating fluids in between meals
  2. Include healing drinks like bone broth and tea with collagen
  3. Stick to a low fiber, low FODMAP and low fat diet until major symptoms subside
  4. Prioritize sleep and aim to get between 9-10 hours per night.


Jesse St. Jean

Jesse St. Jean

I am many things: a wife, a daughter, a sister, a nutritional therapist, a dog-mom… and I’m an autoimmune warrior.

Nutritional therapist Jesse

Hi, I'm Jesse

I empower women autoimmune warriors to reclaim their health by teaching each woman how to make the right food choices to heal her body while confidently owning her journey so she can live a vibrant life with chronic illness.


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