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Gluten Free Pumpkin Cream Cheese Muffins

Gluten Free Pumpkin Cream Cheese Muffins

Published: Sep 29, 2022 by Sandi Gaertner · 7 Comments · This post may contain affiliate links

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a pin of the cream cheese pumpkin muffins.

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!

a pumpkin cream cheese muffin on a small white plate.
Jump to:
  • Why These Muffins Are Great:
  • Recipe Notes:
  • Recipe Step By Step Directions:
  • Praline Topping Option:
  • Tips and Recipe FAQ:
  • More Gluten Free Pumpkin Recipes:
  • 📖 Recipe
  • 💬 Comments

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 These Muffins Are Great:

  1. You get two delicious flavors in one muffin!
  2. These muffins are a show-stopper. They are perfect to serve 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 teaspoon to the cream cheese filling too! ❤️ Yum!"

Vikki B.

Recipe Notes:

Here are the ingredients you will need to make this gluten free pumpkin cream cheese muffins recipe. In some cases, I recommend certain brands. This doesn't mean they are the only brands that work well in this recipe. It just means they are the brands I used and tested myself.

photos of the pumpkin cream cheese muffins ingredients.
  • 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
  • Salt - Use sea salt or kosher salt.
  • Brown Sugar - It is okay to use either light or dark brown sugar.
  • Eggs - Size 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.

Are you ready to make this yummy muffin recipe? Preheat your oven to 425º F for dome top muffins or 350º F for regular topped muffins. Double-check 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 all of your dry ingredients to a large bowl and use a wire whisk to blend them together.

There are two main ways I recommend measuring your flour. I do not use a scale because I find 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: Put the measuring scoop into the flour and fill. Do not pack the flour. 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 together. 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.

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 down to 350º F. This high heat in the first five minutes helps create that dome top.

If you do not want a dome top, just 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.

You can top these with this delicious praline topping too!

Praline Topping Option:

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

  • ⅔ cup chopped pecans
  • ⅓ 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 of my gluten free pumpkin recipes! I have a lot because I really love fall and the pumpkin spice flavors!!

Tips and Recipe FAQ:

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.

I made these today using almond milk. It made 18 good size muffins, moist, and fluffy and delicious. definitely a keeper.

Sylvia M., Pinterest user

More Gluten Free Pumpkin Recipes:

  • Fluffy Gluten Free Pumpkin Cupcakes
  • Gluten Free Pumpkin Pie Bars
  • Gluten Free Pumpkin Donuts
  • Easy Gluten Free Pumpkin Bread

📖 Recipe

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 8 votes
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Prep Time 15 mins
Cook Time 22 mins
Total Time 37 mins
Course Gluten Free Muffins Recipes
Cuisine American
Servings 12 muffins
Calories 548 kcal

Ingredients
  

Muffins

  • 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
  • ⅓ 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

  • ⅔ cup pecans chopped
  • ⅓ cup brown sugar
  • 2 tablespoons butter or sour cream

Instructions
 

  • 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.

Notes

  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.

SPECIAL NOTE

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.

Nutrition

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.

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    Recipe Rating




  1. Colleen

    November 23, 2022 at 5:27 pm

    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!!!

    Reply
    • Sandi Gaertner

      November 23, 2022 at 6:47 pm

      I am so glad your family loved these muffins. If your son bragged about them, it is my highest compliment. Have a great Thanksgiving!

      Reply
  2. Shay

    September 30, 2022 at 10:12 am

    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.

    Reply
    • Shay

      September 30, 2022 at 10:24 am

      Also this recipe made 18 muffins for me standard size.

      Reply
    • Sandi Gaertner

      September 30, 2022 at 11:39 am

      I love you tried both with and without the praline topping :-).

      Reply
  3. Vikki Boyd

    September 30, 2022 at 7:10 am

    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!

    Reply
    • Sandi Gaertner

      September 30, 2022 at 7:15 am

      I am so glad you loved them, Vikki. I really appreciate your coming back to let everyone know.

      Reply

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