These homemade gluten free pumpkin cream cheese muffins are fluffy and light. They are easy to make, and they taste as if they came from a bakery! Make them in under 40 minutes!

I am all about delicious fall flavors! I am really proud of how these gluten free pumpkin cream cheese muffins came out. The cream cheese filling is similar in flavor to a cheesecake, and this creamy filling goes perfectly with the pumpkin and spice!

If you love muffins, I have several incredible gluten free muffins recipes to try!

Why we can’t get enough of these gluten-free pumpkin cream cheese muffins:

  1. You get two delicious flavors in one muffin!
  2. These muffins are a show-stopper. They are perfect for serving family and friends.
  3. If you are a pumpkin spice fanatic like me, you can serve these fluffy homemade muffins all year long.
  4. These muffins freeze really well, so you can always have them on hand.
  5. Top them with the optional praline topping, or enjoy them plain.
  6. You may also want to try these fluffy Gluten Free Pumpkin Chocolate Chip Muffins.

Just made these! Definitely worth the extra effort with the layering and praline topping!! So fluffy and delicious. Instead of just cinnamon we used pumpkin pie spice. Added a tsp to the cream cheese filling too! ❤️ Yum!”

Vikki B., blog comment

Allergen Information:

These homemade pumpkin cream cheese muffins are gluten-free, soy-free, and oat-free. They are nut-free if you omit the praline topping.

Photos of the pumpkin cream cheese muffins ingredients.

Ingredient Notes:

For the full list of ingredients and amounts, please go to the recipe card below.

  • Gluten Free Flour Blend – I have tested this recipe with King Arthur Measure for Measure GF and Bob’s Red Mill 1 to 1 GF blend.
  • Xanthan Gum – If your gluten free flour blend doesn’t contain xanthan gum or guar gum, please add one teaspoon.
  • Baking Powder – I recommend using aluminum-free baking powder
  • Eggs – Use ize large.
  • Pumpkin Puree – Be sure to use pumpkin puree and NOT pumpkin pie filling in this recipe.
  • Milk – You can use regular milk or non-dairy. If you use plant milk, be sure to check the list to ensure it is gluten free.
  • Cream Cheese – I used full-fat cream cheese. If you are dairy-free, try Kite Hill dairy-free cream cheese. Check to see if the cream cheese is gluten free.
  • Oil – I recommend using a light oil like avocado.
  • Spices – Ground pumpkin pie spice and cinnamon give these gluten free pumpkin cream cheese muffins their delicious fall flavors.

Need help with your muffins? I have a great gluten free muffin troubleshooting guide, and here are my favorite tools for making muffins.

Are you ready to make this yummy muffin recipe? Preheat your oven to 425º F for dome-top muffins or 350º F for regularly topped muffins. Double-check that your oven rack is in the middle of the oven position.

Recipe Step-By-Step Directions:

Photos of steps 1 and 2.

Step 1: Add your dry ingredients to a large bowl and blend them together with a wire whisk.

I recommend two main ways of measuring your flour. I do not use a scale because every blend varies in measurement.

Spoon Method: You can also use a spoon to fill the measuring cup. Use a knife to level along the top to remove the extra flour. Leveling Method: Fill the measuring scoop with flour, but do not pack it. Use a knife to scrape along the top to remove the extra flour.

Step 2: Add the wet ingredients to a smaller mixing bowl and whisk to blend them. Pour the wet ingredients into the dry ingredients.

For best results, mix until they are just BARELY mixed. If you overmix your batter, your muffins will not turn out fluffy! I do not recommend using a standing mixer to make these muffins. You can use it for the cream cheese layer but not the muffin batter.

Photos of steps 3 and 4.

Step 3: This is what your pumpkin muffin batter will look like. Set this batter aside while you whip up the cream cheese mixture.

📢 Sandi says: Every gluten-free flour blend has a different starch-to-grain ratio. The brand of gluten-free flour you use will affect the moisture of the batter. If your cake batter is too runny, add more flour, and if it is too thick, add more liquids.
Read Why Gluten-Free Flour Blends Vary to learn more about this.

Step 4: In a small bowl, add the softened cream cheese, sugar, flour, and egg. Use an electric mixer to whip this into a smooth mixture.

A photo of the pumpkin and cream cheese in the muffin pan.

Step 5: Line a muffin pan with parchment paper liners. Fill each halfway with pumpkin batter. Add a dollop of the cream cheese mixture. Top each with the remaining pumpkin batter.

Step 6: Place the muffin pan into the oven and bake at 425º F for 5 minutes, then reduce the oven temperature to 350º F. This high heat in the first five minutes helps create that dome top.

If you do not want a dome top, bake the muffins at 350º F for 20-22 minutes. The baking time may vary depending on the cup size of the muffin pan.

Step 7: Remove the muffins from the oven and place them on a wire cooling rack.

Pumpkin cream cheese muffins with streusel topping on a rack.

Praline Topping Option:

If you would like to make these with a praline topping, add the following to a small mixing bowl:

  • 2/3 cup chopped pecans
  • 1/3 cup brown sugar
  • 1 tablespoon gluten free flour
  • 2 tablespoons of butter or sour cream

Mix well and top each muffin before baking.

If you love pumpkin, use this shortcut to see all my gluten free pumpkin recipes! I have a lot because I really love fall and the pumpkin spice flavors!!

Frequently Asked Questions:

How do you get a dome top when baking muffins?

If you want your muffins to have a domed style top, bake at 425º F for the first 5 minutes, then reduce the temperature to 350º F.

How do you store pumpkin muffins?

Store your pumpkin cream cheese muffins in an airtight container in the refrigerator. They will keep fresh for up to 4 days.

Can you freeze these pumpkin cream cheese muffins?

I recommend freezing these muffins. Place cooled muffins in a zipper-style freezer bag. They will keep fresh for up to 4 months. They can be thawed to room temperature or heated for 35 seconds in your microwave oven.

Why did the muffins turn out dense?

There are two possible reasons for dense muffins. 1. You overmixed your batter, or 2. You used a very starchy gluten free flour blend.

A pumpkin muffin cut in half on a plate.

More Gluten Free Pumpkin Recipes:

Love This Recipe?

If you made and enjoyed this recipe, I would be incredibly grateful if you could leave a comment below. Please include which flour blend you used. This will help others know this recipe is delicious. Thank you!

A pumpkin cream cheese muffin on a small white plate.

Gluten Free Pumpkin Cheesecake Muffins

Sandi Gaertner
Fluffy gluten free pumpkin cheesecake muffins that are absolutely delicious.
5 from 15 votes
gluten free allergy icon
soy free allergy icon
Prep Time 15 minutes
Cook Time 22 minutes
Total Time 37 minutes
Course Gluten Free Breakfast Recipes, Gluten Free Muffins Recipes
Cuisine American
Servings 12 muffins
Calories 548 kcal



  • 2 ½ cups gluten free flour blend * see note
  • 1 ¼ cups brown sugar light or dark
  • 2 teaspoons baking powder aluminum-free
  • 1 teaspoon baking soda
  • 1 ½ teaspoons ground cinnamon
  • ½ teaspoon salt
  • 3 large eggs
  • 12 ounces pumpkin puree
  • 1 cup oil I recommend avocado or canola
  • cup milk or non-dairy milk

Cream Cheese Mix

  • 8 ounces cream cheese room temperature
  • ½ cup sugar
  • 1 large egg
  • 1 tablespoon gluten free flour blend brand doesn't matter

Optional Praline Topping

  • cup pecans chopped
  • cup brown sugar
  • 2 tablespoons butter or sour cream


  • Preheat the oven to 425º F for dome top muffins, or 350º F for regular tops.
  • In a large bowl, add the flour, brown sugar, baking soda, baking powder, powder, salt, and cinnamon. Use a whisk to blend them together.
  • Add the eggs, pumpkin, oil, and milk to a medium-sized bowl. Whisk to blend.
  • Pour the wet ingredients into the dry ingredients. Mix until they are just barely mixed. If you overmix the batter, your muffins will not turn out fluffy.
  • In another bowl, add the cream cheese topping ingredients. Mix well with a whisk or electric mixer.
  • Line a muffin pan with parchment paper muffin liners. Fill each halfway with the pumpkin batter. Add a dollop of the cream cheese mixture. Top with more pumpkin batter.
  • Make the praline topping if you are using it. Top each muffin.
  • Bake at 425º F for 5 minutes, then reduce the temperature to 350º F. Bake for 22-24 minutes, depending on the size of your muffin pan.
  • Remove from the oven and place the muffins on a cooling rack.


  1. I tested this recipe using King Arthur Measure for Measure. Other flour blends should work, but I haven’t tested any others. 
  2. Add one teaspoon if your blend doesn’t contain xanthan or guar gum.
  3. I do not recommend a standing mixer because this will overmix the muffin batter.
  4. Store the muffins in an airtight container in the fridge for up to 4 days.
  5. Freeze the muffins in a freezer bag.


Please know that every gluten free flour blend has a different starch to grain ratio. If you use a blend I didn’t test, you may need to adjust your moisture levels in your baked goods.


Serving: 1muffinCalories: 548kcalCarbohydrates: 60gProtein: 7gFat: 34gSaturated Fat: 7gPolyunsaturated Fat: 7gMonounsaturated Fat: 17gTrans Fat: 0.2gCholesterol: 79mgSodium: 297mgPotassium: 243mgFiber: 4gSugar: 39gVitamin A: 4833IUVitamin C: 2mgCalcium: 120mgIron: 2mg
Tried this Recipe? Pin it for Later!Mention @FearlessDining or tag #FearlessDining!

Nutrition Disclaimer

Nutritional information is an estimate provided to you as a courtesy. You should calculate the actual nutritional information with the products and brands you are using with your preferred nutritional calculator.

5 from 15 votes (11 ratings without comment)

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Recipe Rating


  1. This recipe looks delicious. Can you make it in a square pan. If so what size would be acceptable.
    Thank you.

  2. 5 stars
    These muffins turned out perfect… Light, fluffy and delicious!

    I used baking soda and cream of tartar instead of baking powder. I also added the required baking soda as well. I kept everything else the same.

    Do yourself a favor and bake these muffins. 😁

    I will add this recipe to the items that I bring to potluck events.

  3. 5 stars
    I do not bake much, except for the holidays!
    The recipe was easy to follow and they came out light and fluffy. My son was impressed and loved them. He bragged to his friends about the amazing treat I baked.
    I used half and half for the milk and prepared praline pecans otherwise I followed the recipe.
    I used baking cups and it made 15.
    I may need to bake more!!!

  4. 5 stars
    I made half of these with the praline topping and half without it for the kids. They just don’t know what they are missing out on! This muffin recipe is not as sweet as I normally associate muffins with, but maybe I am just eating sweet muffins. Next time I might add a little more sugar to suit personal preferences.

  5. 5 stars
    Just made these! Definitely worth the extra effort with the layering batters and praline topping!! So fluffy and delicious… The praline topping sends this recipe over the top!! Instead of just cinnamon we used pumpkin pie spice. Added a tsp to the cream cheese filling too! ❤️ Yum! Also if you are using standard muffin tins this makes 2 dozen! And we reduced the cooking time to 21 mins total. 5 min at 425F and 16 mins at 350F. Huge hit with all my family!! Thank you!