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Orange coloured pumpkin cream cheese muffins on a grey board. the cream cheese is oozing out of the sides of the muffin and they are topped with pumpkin seeds.
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Healthy & Homemade Pumpkin Muffins with Cream Cheese Filling (Low FODMAP)

Perfect for fall, back to school, & work snacks. Healthy & homemade pumpkin muffins with cream cheese filling are nutritious and EASY!
Prep Time20 mins
Cook Time20 mins
Total Time40 mins
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.