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Pumpkin Cream Cheese Muffins (Low FODMAP)

5 from 1 vote

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I am excited to share this healthy and homemade pumpkin cream cheese muffin recipe with you! Did I mention that they are also low FODMAP and gluten free? The low FODMAP diet can be challenging. So, I took inspiration from Cookie and Kate’s Pumpkin Muffins to create a low FODMAP version of their 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, it really isn’t challenging to do!

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

Baking these pumpkin cream cheese 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 registered dietitian, 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 pumpkin cream cheese muffin as a great snack for kids, and of course, adults too! Did I mention that they are low FODMAP? Looking for some other yummy snack ideas for kids? Try this cranberry lemon loaf, or these granola bars here!

How do you store cream cheese filled muffins?

Pumpkin cream cheese muffins need to be stored in the refrigerator. After they have been baked, allow them to cool down for about 1 hour on the counter. We recommend storing pumpkin cream cheese muffins in an airtight container in the fridge for about 3-5 days for an easy grab and go snack. You can also try reheating them in the microwave for about 30 seconds or 1 minute (depending on your microwave). It makes them super yummy, fluffy and moist!

Can you freeze cream cheese muffins?

Yes! you can absolutely freeze pumpkin cream cheese muffins. After they’ve been cooked and cooled place them into a freezer safe bag or airtight container into the freezer. This can be a handy option if you make a big batch. Freeze some and then you will have leftovers for a later time. Pumpkin cream cheese muffins can be frozen for up to 2-3 months.

How long can cream cheese muffins sit out?

It is recommended to leave pumpkin cream cheese muffins out for no longer than 2 hours. Because cream cheese can spoil quickly it is important to refrigerate these muffins after they have been cooked. Once they have been cooled (this usually takes less than 1 hour) place the muffins into an airtight container into the refrigerator.

Love this low FODMAP recipe as much as we do? Our collection of low FODMAP recipes were created to help you navigate the low FODMAP diet. Many of our patients have tried implementing the low FODMAP diet on their own. However, this diet should be conducted with the support of a registered dietitian. At Ignite Nutrition we offer one-on-one nutrition counselling to help you start on the low FODMAP diet with guidance.

three orange muffins with pumpkin seeds on top of them sitting on a marble cutting board with a muffin tin full of more muffins in the background.
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5 from 1 vote

Pumpkin Cream Cheese Muffins (Low FODMAP)

Perfect for fall, back to school, & work snacks. These low FODMAP and gluten free pumpkin muffins with cream cheese filling are delicious and EASY!
Prep Time20 minutes
Cook Time20 minutes
Total Time40 minutes
Course: Breakfast/ Snack
Cuisine: American, Breakfast
Diet: Vegetarian
Keyword: low fodmap
Servings: 12
Author: Andrea Hardy


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°F 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.


Other great mix-in options: Walnuts are definitely a good mix in option that add an nice extra crunchy texture. 
Don’t have pumpkin spice mix? Try adding in equal parts cinnamon, nutmeg and ground cloves and ginger. 

**Last reviewed May 2022 for Monash FODMAP portions

Written by Nancy Gammack
University of Alberta Dietetic Intern

Categorized: Low FODMAP, Snacks

One response to “Pumpkin Cream Cheese Muffins (Low FODMAP)”

  1. 5 stars
    Can’t wait to make these this fall!! I love pumpkin spiced foods/drinks so this is definitely going to be a recipe for me to try 😋

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