Healthy Chocolate Chip Pumpkin Muffins 

These healthy chocolate chip pumpkin muffins are sure to “wow” your friends and family this holiday season, whether or not they have Crohn’s disease or ulcerative colitis!

Why This Recipe is IBD-Friendly

These healthy chocolate chip pumpkin muffins are friendly for a variety of dietary restrictions related to common Crohn’s and ulcerative colitis food triggers. They’re:

  • Gluten-free
  • Dairy-free
  • Nut-free
  • Egg-free
  • Corn-free
  • Soy-free
  • Vegan and vegetarian

Nutrition Benefits of These Chocolate Chip Pumpkin Muffins

Additionally, this recipe is packed with substantial amounts of two nutrients that are commonly deficient in IBD warriors: vitamin A and iron. Just one muffin contains:

  •  64% of the daily value of vitamin A thanks to the pumpkin in this recipe
  • 14% of the daily value of iron thanks to the ground flaxseed and cocoa powder/dark chocolate chips

Finally, these muffins pack in anti-inflammatory nutrients while being low in sugar (10 grams per serving) and fiber (3 grams per serving). This is beneficial since these nutrients may not be tolerated well in high amounts during an IBD flare. 

One serving also contains 4 grams of protein, a macronutrient that IBD warriors may need more of compared to a person without the condition.

Important Tips to Make These Muffins

Choosing Your Chocolate Chips:

Did you know that many dark chocolate chips contain dairy and food additives that may not be tolerated by people with IBD?

While we’re not paid or sponsored by any food or brand company, here are a few of our favorite IBD-friendly, dairy-free and emulsifier-free dark chocolate chip brands:

  • Enjoy Life Dark Chocolate Morsels
  • Hu Chocolate Dark Chocolate Gems
  • Good & Gather (Target Brand) Organic Dark Chocolate Baking Chunks
  • Amanda’s Own Chocolate Mini Chips

Not a Fan of Coconut Oil?

Avocado oil can also work well in this recipe, as it has a neutral flavor profile, has a high smoke point, and is an anti-inflammatory oil.

How to Store Your Homemade Muffins

One serving of this recipe equals 1 muffin. If making a full batch of this recipe, you can refrigerate these muffins in an airtight container for up to five days, or place them in an airtight freezer bag for up to two months.

How to Make Pumpkin Chocolate Chip Muffins

Because this recipe is egg-free, the first step will be to make a flax “egg.” Mix the ground flax seed with water and allow it to sit for five minutes until thickened. 

To the same bowl, mix in the pumpkin, non-dairy milk, sugar and oil. Then add in the remainder of the ingredients: oat flour, cocoa powder, pumpkin pie spice, baking powder and soda, and salt. Fold in chocolate chips (optional). Fill in the muffin tray, bake, and enjoy!

An up close image of chocolate chip pumpkin muffins

Healthy Chocolate Chip Pumpkin Muffins

Danielle Gaffen, MS, RDN, LD
These healthy chocolate chip pumpkin muffins are sure to “wow” your friends and family this holiday season, whether or not they have Crohn’s disease or ulcerative colitis!
Total Time 35 minutes
Course Dessert, Snack
Cuisine American
Servings 12
Calories 189 kcal


  • 1 Muffin Tray
  • 12 Muffin liners
  • 1 Bowl Large
  • 1 oven


  • 1 tbsp Ground Flax Seed
  • 3 tbsps  Water
  • 1 can Pureed Pumpkin
  • 1/4 cup Oat Milk
  • 1/3 cup Coconut Sugar
  • 1/4 cup Coconut Oil
  • 1 1/3 cups Oat Flour
  • 1/2 cup Cocoa Powder
  • 2 tsps Pumpkin Pie Spice
  • 1 tsp Baking Powder
  • 1/2 tsp Baking Soda
  • 1/4 tsp Sea Salt
  • 1/2 cup Dark Chocolate Chips (optional)


  • Preheat the oven to 350ºF (177ºC) and line a muffin tray with liners or use a silicone muffin tray.
  • In a large bowl combine the ground flax and water. Let it sit for five minutes or until thickened.
  • To the same bowl, add the pumpkin, oat milk, coconut sugar, and coconut oil. Mix until smooth. Then add the oat flour, cocoa powder, pumpkin pie spice, baking powder, baking soda, and salt. Stir well until combined. Fold in the chocolate chips, if using.
  • Fill each muffin liner about 3/4 full and place in the oven to bake for 22 to 25 minutes, until cooked through. Remove from the oven and let cool before serving or storing. Enjoy!


Refrigerate in an airtight container for up to five days. Place in an airtight freezer bag for up to two months.
Serving Size
One serving is equal to one muffin.
No Oat Milk
Use almond milk.
Additional Toppings
Chopped pecans or walnuts.


Serving: 1MuffinCalories: 189kcalCarbohydrates: 23gProtein: 4gFat: 10gSaturated Fat: 8gMonounsaturated Fat: 1gSodium: 146mgPotassium: 107mgFiber: 3gSugar: 10gVitamin A: 3178IUVitamin C: 1mgCalcium: 50mgIron: 2mg
Keyword corn-free, dairy-free, egg-free, gluten-free, nightshade-free, nut-free, soy-free, vegan, vegetarian

Looking for more IBD-Friendly Desserts?


About the Author

Picture of Danielle Gaffen, MS, RDN, LD

Danielle Gaffen, MS, RDN, LD

Understanding the link between nutrition and gut disease prompted me to obtain my master’s degree in Nutritional Sciences at San Diego State University and become an IBD Registered Dietitian Nutritionist. Now I work with people who have Crohn’s and colitis who are struggling with confusion around what to eat. My favorite part is helping them to build confidence to eat without fear while managing their symptoms.

Explore more recipes

Food Survival Guide During an IBD Flare

Learn 9 key food tips from IBD dietitian Danielle Gaffen to help get you through a flare and reduce symptoms.

By completing this form you also agree to receive our IBD newsletter. Unsubscribe at any time.