Gluten-Free Cream Cheese Stuffed Pumpkin Muffins

Pumpkin isn’t just for fall. Sure, you may have overdosed on pumpkin spice lattes this year. And sure, it was probably sickening yet amazing. But once you move past the withdrawal, you can get into the real pumpkin flavours of the winter season.

Baking with gluten-free flours is always risky. I was pretty confident in this recipe because pumpkin is very naturally moist which helps keep the mix from crumbling when baking. Also, stuff anything with this cream cheese filling and I won’t complain. I had to stop myself from eating it on it’s own (and failed).

Some of the most important tips of the recipe:

  1. Chill the cream cheese filling.
  2. Follow the ratio of batter to filling.
  3. Allow them to cool.

I adapted this recipe from The Girl Who Ate Everything. The main change was the switch from regular to gluten-free flour. For this recipe, I tried out the newer Robin Hood GF mix which I found has a pretty good texture for baking and acts as a nice substitute. You can still definitely taste the difference, but not so much that it would be off-putting.Gluten-Free Pumpkin Muffins with Cream Cheese Filling

Gluten-Free Pumpkin Muffins with Cream Cheese Filling


Makes 24 muffins

For the filling:
  • 8 oz. cream cheese, softened
  • 1 cup confectioner’s sugar
For the muffins:
  • 3 cups gluten-free all-purpose flour
  • 1 tsp. ground cinnamon
  • 1 tsp. ground nutmeg
  • 1 tsp. ground cloves
  • 1 tbsp. plus 1 tsp. pumpkin pie spice
  • 1 tsp. salt
  • 1 tsp. baking soda
  • 4 large eggs
  • 2 cups sugar
  • 2 cups pumpkin puree (see Note)
  • 1 1/4 cups vegetable oil
For the topping:
  • 1/2 cup sugar
  • 5 tbsp. all-purpose gluten-free flour
  • 1 1/2 tsp. ground cinnamon
  • 4 tbsp. cold unsalted butter, cut into pieces


For the filling:

Mix the cream cheese and powdered sugar in a medium bowl until smooth and no lumps remain. Transfer the mixture to a piece of plastic wrap and shape into a log about 1½-inches in diameter. Smooth the plastic wrap tightly around the log, then put in the freezer and chill until at least slightly firm, about 2 hours. The mixture should be firm enough to cut with a knife.

For the muffins:

Preheat the oven to 350 degrees F. Line muffin pans with paper liners. In a medium bowl, combine the flour, cinnamon, nutmeg, cloves, pumpkin pie spice, salt and baking soda; whisk to blend. In the bowl of an stand mixer combine the eggs, sugar, pumpkin puree and oil with the paddle attachment. Mix on medium-low speed until smooth. With the mixer on low speed, add in the dry ingredients, mixing just until incorporated. Do not overmix.

For the topping:

Mix the sugar, flour and cinnamon in a small bowl; whisk to blend. Add in the butter pieces and mix with your hands until it is coarse and crumbly, so that it looks like the texture of wet sand. Transfer to the refrigerator to chill until ready to use.


Fill each muffin well with a small amount of batter, just enough to cover the bottom of the liner (1-2 tablespoons). Slice the log of cream cheese filling into 24 equal pieces. Place a slice of the cream cheese mixture into each muffin well. You want to put the cream cheese lower than you think because it will rise a lot during the baking process. Divide the remaining batter among the muffin cups, placing on top of the cream cheese to cover completely. Sprinkle a small amount of the topping mixture over each of the muffins.

Bake for 20-25 minutes. Transfer to a wire rack and let cool completely before serving. Store in an airtight container for up to a week.

Gluten-Free Pumpkin Muffins with Cream Cheese Filling

5 Comments Add yours

  1. Beautiful, with a nice little surprise – these look great!

  2. trixpin says:

    These look so good 🙂 I don’t think I’ve ever made a muffin with a filling pre-baked into it, especially not cream cheese; it sounds amazing! And I’m glad to see pumpkin recipes still floating around – I don’t think you can ever have too much pumpkin 🙂

  3. Love it!! Looks delicious. Every dessert with a surprise inside is like 10x better. Plus the combination cream cheese + pumpkin = to die for!

  4. Dragos Balan says:

    This blew my mind! I think i was pondering its awesomeness for days. I couldnt even tell it was gluten free!

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