Gluten Free Pumpkin Cheesecake Muffins

Pumpkin & Cream Cheese. They just go together so nicely. There are so many great recipes out there that combine these two flavours. I’ve seen recipes for gluten free Pumpkin Cheesecake Muffins all over the internet, and decided to give them a try. I really liked them, the cream cheese baked down into the muffins slightly, making it a nice moist, flavourful muffin.

Gluten Free Pumpkin Cheesecake Muffins
Serves: 24
As good as, if not better, than Starbucks, but gluten-free.
  • 3 cups all-purpose gluten-free flour (see note)
  • 1 1/2 teaspoons xanthan gum
  • 3 teaspoons ground cinnamon
  • 1 1/2 teaspoon ground nutmeg
  • 1 teaspoon ground ginger
  • 1 teaspoon ground cloves
  • 1 teaspoon salt
  • 1 teaspoon baking soda
  • 4 large eggs
  • 1 cup granulated sugar
  • 1 cup brown sugar
  • 2 cups cooked or canned pumpkin puree (not pie filling)
  • 1/2 cup oil
  • 3/4 cup apple sauce
  • 8 oz. package cream cheese
  • 1/3 cup granulated sugar
  • Chopped nuts (walnuts, pecans) or pumpkin seeds to top (optional)
  1. Preheat oven to 350 degrees F.
  2. In a small bowl, beat cream cheese and 1/3 cup white sugar until light. Set aside.
  3. In a large bowl, combine flour, xanthan gum, spices, salt and baking soda. Set aside.
  4. In a medium mixing bowl, combine the eggs, 1 cup white sugar, brown sugar, pumpkin puree, vegetable oil, and apple sauce.
  5. Pour wet ingredients into dry ingredients, stirring just until combined.
  6. Fill muffin tins (greased or lined with paper cups) half full. Put 1-2 tsp cream cheese mixture in the middle, pressing down slightly.
  7. Sprinkle with 1 tsp chopped nuts or pumpkin seeds.
  8. Bake in preheated oven for 20-25 minutes, until a toothpick comes clean from the muffin part (do not touch the cream cheese, it is very hot!).
  9. Let cool in pans for 5 minutes before removing to racks to cool completely.
The flour blend I use is 4 cups superfine brown rice flour, 1 1/3 cups potato starch (not flour), 2/3 cup tapioca starch. Combine all ingredients in a large zipper-top bag. Shake until well blended.


Don’t forget, you can still download the FREE Holiday E-book by clicking the picture below. With nearly 40 gluten-free baking recipes, you are sure to find a few that will become part of your holiday traditions.


  1. I Am Gluten Free says

    These look lovely. I can practically smell the pumpkiny smell of the muffins baking. I love the added touch of the pumpkin seeds! Nice job!

  2. Stephanie says

    Oh my, I am definitely trying these as soon as I've finished the pumpkin cheesecake in my fridge! I swear, you're trying to make me fat! Gorgeous photo as well 😀

  3. Kate says

    This was perfect timing. I was at Starbucks and saw their pumpkin cheesecake muffins and thought I needed to figure out how to make those gluten free, but thanks to you I can just make them with confidence!
    Thank you so much!

  4. Tami says

    Thank you! I’ve been looking online for pumpkin muffins with chream cheese filling and couldn’t find but one other and it just wan’t saying “bake me”.=) Thought I’d give your site a whirl and sure enough, you have the perfect recipe! These are in the works now!

  5. Michelle says

    These are FANTASTIC! yum, yum yum! Just a note, you forgot to include when to add the xanthan gum. I assumed to do it in step 2 with the other dry ingredients but I could see people forgetting to add it since it’s not in the directions. Would hate for anyone to make this and have it be a flop! Soooo good!

    • Jeanine says

      Ah, thanks for catching that! I edited the recipe to include that. I’m glad that you like them, I have some sitting on my counter right now as well, calling out to the cup of coffee in front of me. I may need to do something about that. 😉

  6. Erin J. says

    I just made these last night and they are a huge hit in our house! I sprinkled flax seeds on top which add even more nutrition and are kid friendly for our preschooler and toddler. My gluten-free husband said they are absolutely delicious and I think has already eaten 6 in the 24 hours since I made them. Thank you for posting such a great recipe!

    Next time, I’m going to try putting the cream cheese in the middle (fill muffin cup half full of batter, drop in cream cheese, cover in batter) and sprinkle flax seed+cinnamon+sugar on top before baking. Hoping this will make them “lunch box proof” and hopefully make them freezable. :)

    Also, one tip I’ve found for higher muffins tops is to fill the cups to the rim (instead of 1/2 to 3/4 full) and bake at 400F for 15 mins then turn oven down to 350F for the remainder time (I did 5-7 mins for this recipe). No matter which recipe I’ve used (GF or not), this technique works and the resulting muffins are gorgeous, taller and the tops are pleasantly crunchier! Just thought I’d share in case anyone wanted to give it a shot.

    • Merle says

      so I tried your tip…but didn’t realize until it was too late, I only got 18-20 muffins and had extra filling – so accomodate as necessary. thanks for the info!

  7. AllieSong says

    Thank you for the wonderful recipes! I made both these, the Pumpkin Cheesecake muffins and the Lemon Poppy Seed Muffins, for an even at the kids school. They both turned out excellently. The Pumpkin Cheesecake Muffins are so beautiful, they disappeared first! Thanks again!

  8. Lorna says

    These look absolutely devine. I am about to make them tomorrow morning, but when I look through the recipe I see that it only calls for 1 tsp of baking soda. That seems less than I;m used to usigng in muffins (usuallt use baking powder). Since I plan on taking them to a special event I just wanted to check before I make them. My mouth is watering!

  9. Lorna says

    Oh, Jeanine, how could I ever have doubted you???? They were absolutely marvelous. I took them to an agility trial yesterday and everyone was loving them and asking for the recipe…they couldn’t believe that they weree gluten free!. We have another trial next weekend…so now I have to figure out what to make to keep everyone as happy as these did….I’m open for suggestions.

  10. Holly says

    Oh my goodness! These were so delicious! My friends said they were one of the best pumpkin muffins they ever had before they knew they were gluten free! And my family was so happy that I FINALLY made a successful gluten free muffin. I’m going to make a ton of these this fall. Highly recommend!

    • says

      Don’t you just love it when those that don’t need to eat gf still love it? AWESOME! 😀 Thanks so much for sharing your success story, Holly, I appreciate it!


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