These high protein Grain Free Pumpkin Cheesecake Muffins with a maple cheesecake topping are so soft and delicious. They’re easy to make, naturally sweetened, nut-free and perfectly spiced.
Pumpkin muffins are perfect for fall!
Pumpkin muffins have been my favorite since I was a young kid.
My mom and I always used to get the most delicious pumpkin muffins at The Nut Tree or The Coffee Tree, one of California’s most legendary road stops. The original Nut Tree is long gone now. It was the perfect road stop between Sacramento and San Francisco. We used to go there often because it was on the way to, or back from my grandma’s house in Vallejo.
No matter what, we always stopped there. Even if we didn’t stop to sit down and eat at The Nut Tree, we ALWAYS stopped to buy pumpkin muffins and their famous honey gingerbread cookies.
Oh they were so good! Seriously the best treats ever.
Pumpkin plus cheesecake?! Yes please!
Those pumpkin muffins will always hold a special place in my heart. Now, every time I make pumpkin muffins, I think of my beautiful mom, missing her, and knowing she would love these muffins too.
Those Nut Tree muffins are a thing of the past, but that doesn’t stop me from enjoying pumpkin muffins now. Especially pumpkin muffins topped with delicious maple cheesecake!
Pumpkin muffins in my opinion should be well spiced, super soft and tender. Top them with a bit of cheesecake and you have a winner!
Gluten is a thing of the past for me, so instead I use my favorite gluten free and grain free flour, cassava flour for these muffins. It’s very similar to regular flour with the bonus of being a resistant starch when eaten cool {resistant starch = prebiotics that feed probiotics + supports digestion and the gut}.
To keep these muffins extra soft and moist, I use my favorite nourishing grass-fed collagen. I love using it for baking because it helps keep baked goods nice a soft. Plus it adds protein!
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Fall is just around the corner! Bring on the pumpkin goodness and enjoy these delicious, protein packed Grain Free Pumpkin Cheesecake Muffins!
Grain Free Pumpkin Cheesecake Muffins

Grain Free Pumpkin Cheesecake Muffins
These high protein Grain Free Pumpkin Cheesecake Muffins with a maple cheesecake topping are so soft and delicious. They're easy to make, naturally sweetened, nut-free and perfectly spiced.
Ingredients
Muffins:
- 1 cup pumpkin puree
- 1/3 cup grass-fed butter or ghee, melted or avocado oil
- 1/2 cup maple syrup
- 1/4 cup organic applesauce or 1 small organic apple, peeled
- 1 teaspoon vanilla extract
- 2 pastured or organic eggs, room temperature
- 1 3/4 cup cassava flour (<-- this is the only cassava flour I use and recommend)
- 1/3 cup grass-fed collagen (<-- this is the only grass-fed collagen I use and recommend)
- 2 teaspoons ground cinnamon
- 1 teaspoon baking soda
- 1/2 teaspoon sea salt (<-- this is my favorite sea salt)
- 1/2 teaspoon ground ginger
- 1/8 teaspoon ground cloves
Cheesecake Topping:
- 6 tablespoons organic cream cheese, room temperature
- 6 tablespoons maple sugar {<-- this is my favorite brand}
Instructions
- Preheat oven to 350 degrees F. Line muffin pan with muffin wrappers. Set aside.
- Add all wet ingredients to blender or food processor {you could also use a hand held mixer and mixing bowl instead} - pumpkin, melted healthy fat of choice, maple syrup, applesauce {see note}, vanilla and eggs. [Note: If you're using a whole apple instead of applesauce, add it to the blender or food processor first. Blend until pureed. Then add remaining wet ingredients.] Pulse just until combined, about 3-5 seconds. Set aside.
- Add all dry ingredients to a large mixing bowl. Stir to combine. Pour wet pumpkin mixture into dry ingredients. Stir to combine, just until incorporated. Evenly distribute pumpkin batter in muffin wrappers. Set aside.
- In a mixing bowl, combine softened cream cheese and maple sugar. Mix until fully combined. Add a spoonful, about 1 tablespoon of the "cheesecake" mixture to the tops of each pumpkin muffin batter. You can leave the mixture just sitting on the top or you can use a knife to gently swirl some of the cheesecake mixture into the pumpkin batter.
- Bake for 15 minutes or until no more than a few moist crumbs comes out on a toothpick. Allow muffins to rest in muffin pan for 5 minutes, then carefully remove from muffin pan to a cooling rack.
Notes
YOU WILL NEED: Large Mixing Bowl, Handheld Mixer/Blender/Food Processor, Muffin Wrappers, Muffin Pan
Storage: Freeze for later use or store in the refrigerator up to 3 days.
Dairy-Free Version: Use avocado oil in the muffins and use a dairy-free (preferably soy-free) cream cheese instead.
Recommended Products
Nutrition Information:
Yield: 12 Serving Size: 1Amount Per Serving:Calories: 280Total Fat: 13gSaturated Fat: 7gTrans Fat: 0gUnsaturated Fat: 5gCholesterol: 60mgSodium: 327mgCarbohydrates: 37gFiber: 2gSugar: 18gProtein: 6g
This nutritional information was auto-generated based on serving size, number of servings, and typical information for the ingredients listed. To obtain the most accurate representation of the nutritional information in a given recipe, please calculate the nutritional information with the actual ingredients and amounts used, using your preferred nutrition calculator. Under no circumstances shall the this website and the author be responsible for any loss or damage resulting for your reliance on the given nutritional information. You are solely responsible for ensuring that any nutritional information provided is accurate, complete, and useful.
Are you on Pinterest? I pin lots of yummy real food recipes + more there. I have a board just for Gluten Free Treats! Come follow along.
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Emily, these look great!! Huge congrats having your site up again, too!! YAY!!! 🙂
Thank you Megan! I’m SO happy to be back xo
Oh gosh! I am totally ready for pumpkin everything after reading this! Love it!
Thanks! Is it getting cooler there?
We love pumpkin! And have been trying to eat more grain free. Thank you!
Pumpkin is awesome! 🙂
These are gorgeous and I am so glad your blog is back!
Thanks so much Linda! I’m so happy it’s back too! xo
Love the cassava flour base! These sound so wonderful to ring in PUMPKIN season!
Thanks! Gotta love pumpkin season 🙂
Oh. my. goodness. These sound wonderful, Emily! How can I say now to pumpkin + cheesecake? Definite win for me!
Pumpkin + cheesecake is up there with chocolate Raia 😉 xo
IS THEIR A FLOUR I COULD USE INSTEAD OF THE CASSAVA FLOUR AND BE EQUALLY AS GOOD? I HAVE SO MANY FLOURS ON HAND.
Hi Carole, you could try using a gluten free blend, but I haven’t tried one at this point. Coconut flour for sure will not work though and I’m not sure if almond flour will work the same. Otto’s cassava flour is closest to regular flour in consistency. I hope that helps! 🙂
DE-LISH! I bet I could totally make the cheesecake using dairy-free cream cheese too!
Yes for sure! 🙂
Really fab food photography! And, so in season! YUM!
Thank you so much Megan, so kind of you!
pumpkin and cheesecake is always a good idea! Love that these muffins seem sinful, but are actually healthy! Great recipe Emily!
Thanks so much Bethany! xo
Yummy!!! Need to try this recipe ASAP 🙂
I hope you get to try some Katie 🙂
Yum! I’m so ready for all things pumpkin! Bring it on!
Yes! It’s that time for sure 🙂
I finally bought a bag of Cassava flour and now I have a fun recipe to try with it.
Yay! I’m so excited for you! Enjoy it! 🙂
Love the high protein. I would probably leave off the topping and just serve them like this for snack or breakfast.
They’re still yummy without it too 🙂 I make them that way and serve them with some grass-fed butter on top.
reading this has me so excited for Fall! not only do these look amazing but I am sure they taste delicious too!
Thanks Chanel 🙂 Love that fall is on the way!
It’s getting to be that time of year! I’ll be putting this on my fall baking to-do list!
Enjoy! It sure is, fall is on the way 🙂
I don’t have cassava flour… anything I can sub in? I’ve got lots of other flours… go figure I wouldn’t have THE ONE flour you call for… any suggestions?
Hi Kimberly 🙂 Well, I haven’t experimented using other flours with this one yet. It’s possible a gluten free flour blend would work. Coconut flour will not work for sure and it’s possible almond flour might not work too. I hope that helps some.
These look delicious! I am so ready to start baking all things pumpkin!!
Thanks! Yay for baking all things pumpkin! 🙂
So ready for fall with these! They look amazing!
Thanks so much Evi 🙂
Yay a pumpkin recipe!! Love the idea of these cheesecake muffins!
Thanks Madeline 🙂
These look so good! I can’t wait to try these now that fall is upon us!
– Cait
Thank you so much! Yes, fall is in the air 🙂
These look amazing and perfect for fall. I will also check out that collagen since I have been looking for a new brand to try, I use it in my smoothies.
You’ll love their brand Lauren! 🙂 And thank you, so fun for fall.
your food pics are amazing! I so want to try these they sound yummy
Thank you so much, so kind of you. Hope you get to try some 🙂
Oh gosh these look good, I love pumpkin muffins! I love that these are grain free!
Thank so much Bella! 🙂
I love pumpkin muffins & healthy recipes! So this is perfect, cannot wait to try!!
I hope you get to try some Julie 🙂
Pumpkin and cheesecake is always a winning combo and they look terrific!
Yes! Love the combo! Thank you 🙂
Hi There, I’m going to try these out today!
Were are you in the bay area? I grew up in Antioch, moved around the bay area, lived in Vallejo for 5 years now in Napa. Did you attend Bauman Holistic Nutrition College in Emeryville?
Small world 🙂 I’m not in the Bay Area, but grew up part time in SF as kid. My hometown is Sacramento though. No, I didn’t go to nutrition college there. 🙂
Oh my gosh, these look absolutely incredible! xx
Thank you! 🙂
I love pumpkin muffins. Fall is my favorite season because it’s also pumpkin season. These look delicious. Can’t wait to try them.
Thanks so much! I love pumpkin season too 🙂
You have officially got me in pumpkin mode now w/ these beauties!
Aww thanks Christine! I hope you get to enjoy some pumpkin yumminess soon 🙂
These look amazing! And I love that they’re made with such high quality ingredients. 🙂 I’m feeling ready to finally get some of this flour, but I can’t decide whether to get the 2 lb. or 5 lb. bag to start. I don’t bake desserts as often as you, that’s for sure!
Thanks Elaina! Well, that’s a tough decision. I would say go with the 5 lb. bag because you can make other yummies like tortillas. Or play it safe and get the 2 lb. bag to see if you like it first. I LOVE it! It’s my favorite now. I hope you enjoy it when you get some. xo
Love the pumpkin + cheesecake flavors together! Pinned!
Thank you Dena! And thanks so much for the pin. 🙂
Hi! I’m new to using cassava flour. I am making these right now and the batter is super thick. Is that normal?
It’s so thick it’s crumbling, yet soft. Does that make sense?
Hi Pamela, cassava flour batters can be thicker – it just depends on the recipe. This batter is a thicker batter because of the pumpkin puree. I hope that helps. Usually cassava flour needs a bit more moisture and in this recipe the pumpkin adds that moisture.
These look so good! On my pumpkin recipe making list!