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Low FODMAP Pumpkin Cream Cheese Muffins

Healthy & Easy Recipes, Healthy Eating, Low FODMAP & Gut Health Recipes | September 8, 2020

A beautiful rainbow of different fruit and vegetables in a pile.
Low FODMAP Pumpkin Cream Cheese Muffins Featured Image

Hey there, it is Nancy here and I am excited to share a Low FODMAP pumpkin muffin recipe with you just in time for back to school (and of course pumpkin spice season)!

Everyone should enjoy pumpkin season, even low FODMAPPER’s, which is why I decided to modify Cookie and Kate’s Pumpkin Muffins to make a Low FODMAP recipe. Plus, I added a cream cheese filling which I find turns a satisfactory muffin into a fancy one! Even though this Low FODMAP muffin appears fancy, even though it really isn’t challenging to do!

These Low FODMAP pumpkin muffins are a great snack to make on the weekend and then enjoy throughout the school and work week.

Baking these muffins can also be a fantastic activity to do with your kids, or for your kids to make on their own, if they are ready! As a Dietetic Intern, I am so passionate about getting kids in the kitchen and developing culinary skills at a young age. These skills can support developing positive nutrition habits going forward in life.

In addition, baking can be a great way for kids to practice a variety of skills that we often don’t think about! Depending on their age level, this could include practicing their literary skills when reading the recipe, their math skills when reading and measuring fractions of ingredients, and even fine and gross motor skills when blending ingredients and pouring batter! Bring the classroom to the kitchen and include your kids in the meal prep this week!

Enjoy these Low FODMAP Pumpkin Cream Cheese Muffins as a great snack for kids, and of course, adults too!

Low FODMAP Pumpkin Cream Cheese Muffins

Pumpkin cream cheese muffins on a grey board.
Pumpkin cream cheese muffins on a grey board.
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Low FODMAP Pumpkin Cream Cheese Muffins

Prep Time20 mins
Cook Time20 mins
Total Time40 mins
Servings: 12


Cream Cheese Filling Ingredients

  • ¼ cup icing sugar
  • ½ cup /125 grams of cream cheese
  • 1 egg yolk
  • ½ tsp vanilla extract

Muffin Ingredients

  • 2 eggs
  • cup cooking oil, canola or melted coconut oil
  • ½ cup maple syrup
  • 1 cup pumpkin purée
  • ¼ cup of lactose free milk, or a milk alternative, for example; almond milk
  • 1 tsp vanilla extract
  • 1 ¾ cup of gluten free flour (I used Bob Red mill’s all-purpose blend)
  • ½ cup old fashioned oats
  • 2 tsp pumpkin spice blend
  • 1 tsp baking soda
  • ½ tsp salt
  • Pumpkin seeds, for sprinkling (optional)


  • Preheat the oven to 325 degrees Fahrenheit and line a 12 cup muffin pan with paper liners, or grease each cup.
  • Start with the cream cheese filling by blending icing sugar, cream cheese, egg yolk and ½ tsp of vanilla extract into a medium bowl. Using an electric mixer, blend until smooth. Place this filling in the fridge until ready to use so that it stays firm.
  • In a large bowl, whisk 2 eggs. Add in oil, maple syrup, pumpkin puree, milk and vanilla extract. Stir well.
  • In a new bowl, blend all dry ingredients by adding flour, oats, pumpkin spice blend, baking soda and salt together.
  • Slowly add the dry ingredients to the wet and stir until just mixed.
  • Start filling the muffin tins by adding 1 heaping TBSP of pumpkin batter to each muffin cup. Next, add 1 tsp of cream cheese filling to each muffin cup. Lastly cover with pumpkin batter so that each muffin cup is ¾ full. (Optional: sprinkle each muffin with pumpkin seeds).
  • Place in oven and bake for 20-22 minutes.
  • Store muffins in the fridge once cooled.

**Last reviewed May 2022 for Monash FODMAP portions

Pumpkin cream cheese muffins on a grey board.
Written by Nancy Gammack
University of Alberta Dietetic Intern

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