These Keto Pumpkin Cheesecake Muffins are soft, warmly spiced, and filled with a creamy cheesecake swirl in every muffin. The pumpkin keeps the muffins tender, while the cream cheese filling adds just enough richness to make every bite feel a little special.
I especially love these during fall because you get pumpkin, cheesecake, and warm spice all in one bite. They’re perfect with a cup of coffee, but they also look right at home on a fall or Thanksgiving dessert table.
- Is Pumpkin Keto-Friendly?
- Why You’ll Love These Keto Pumpkin Cheesecake Muffins
- Ingredients for Keto Pumpkin Cheesecake Muffins
- How to Make Keto Pumpkin Cheesecake Muffins
- Tips and Variations
- How to Store Pumpkin Cheesecake Muffins
- Can I Make Mini Pumpkin Cheesecake Muffins?
- More Keto Pumpkin Recipes
- Keto Pumpkin Cheesecake Muffins
They’re naturally gluten-free, low-carb, and made without added sugar. Think of them as bakery-style pumpkin cream cheese muffins with a keto-friendly twist.
If you love pumpkin baking, try my Keto Pumpkin Cream Cheese Bread or Keto Pumpkin Muffins next.
Is Pumpkin Keto-Friendly?
Yes. Pumpkin can fit into a keto diet when used in a moderate portion. This recipe uses ¾ cup pumpkin puree across 12 muffins, and each muffin comes to about 4g net carbs based on the nutrition information in the recipe card.
Make sure you use 100% pure pumpkin puree, not pumpkin pie filling, which already contains sweeteners and spices.
Why You’ll Love These Keto Pumpkin Cheesecake Muffins
- Pumpkin and cheesecake in every muffin: The pumpkin batter is layered and gently swirled with a creamy cheesecake filling.
- Creamy cheesecake center: Each muffin has a swirl of cream cheese filling running through it.
- Full of fall flavor: Pumpkin pie spice gives them that warm, cozy flavor you want in a pumpkin muffin.
- Low carb: Each muffin has about 4g net carbs based on the recipe card.
- Gluten-free: They’re made with almond flour and coconut flour or protein powder rather than wheat flour.
- Easy to customize: Add sugar-free chocolate chips, chopped nuts, or adjust the spices to suit your taste.
Ingredients for Keto Pumpkin Cheesecake Muffins
Here’s what you’ll need to make these gluten-free pumpkin cheesecake muffins.
For the Pumpkin Muffin Batter
- Eggs – Use large, room-temperature eggs to help the batter mix smoothly and create a better rise.
- Almond Flour – Superfine, blanched almond flour is essential for a light, fluffy texture. It’s a keto baking staple!
- Coconut flour – A small amount goes a long way—it helps absorb extra moisture for perfectly structured muffins.
- Pumpkin Puree – Make sure it’s pure canned pumpkin puree with no added sugars or spices. The real deal is all you need!
- Pumpkin Pie Spice – A pre-made blend is convenient, but you can also make your own using our recipe for homemade pumpkin pie spice.
- Heavy Cream – Adds moisture and richness to the batter, keeping the muffins soft and tender.
- Sweetener – Erythritol works beautifully, but monk fruit or allulose are great alternatives. Pick your favorite keto-friendly sweetener!
- Butter – Butter not only adds richness but also keeps the muffins moist and flavorful.
- Vanilla Extract – Use pure vanilla extract for that subtle, sweet depth of flavor—an essential in any good bake.
- Baking Powder – Helps the muffins rise, making them light and fluffy.
For the Cheesecake Filling
- Cream Cheese – Go for full-fat cream cheese—it’s the key to a rich, creamy, and luscious filling that takes these muffins to the next level.
- Egg – Just one egg binds the filling together, adding extra creaminess and ensuring a smooth texture.
- Sweetener – A powdered sweetener like erythritol or monk fruit works best to avoid lumps and keep the filling velvety.
- Almond Flour – A small amount helps stabilize the filling and gives it just a touch of texture—perfect for keto baking.
- Vanilla Extract – A splash of pure vanilla enhances the flavor, making the filling irresistibly delicious.
How to Make Keto Pumpkin Cheesecake Muffins
These muffins are ridiculously easy to make (yes, even with that luscious cheesecake center). With just 10 minutes of prep and a handful of simple steps, you’ll have a batch of cozy, sugar-free muffins ready to impress. Let’s do this!
Prepare the Muffin Tin
Preheat the oven to 350°F (180°C).
Line a standard 12-cup muffin tin with paper or silicone liners, or grease the muffin cups well.
Pro Tip: Silicone liners are a game-changer. Muffins pop out effortlessly and look picture-perfect every time!
Make the Pumpkin Muffin Batter
Start by whisking your eggs until smooth—they blend better at room temperature, so if you’ve got the time, let them sit out for a bit.
Next, add the pumpkin puree, cream, sweetener, softened butter, and a splash of vanilla extract. Whisk everything together until silky smooth.
Now, stir in your dry ingredients—almond flour and coconut flour—until the batter comes together. You’re aiming for a thick, creamy consistency that’ll bake up beautifully.
Pro Tip: Sift the almond and coconut flour before mixing. It’s a small step, but it makes a huge difference in avoiding lumps.
Prepare the Cheesecake Filling
In a separate bowl, beat your cream cheese until it’s smooth and creamy. (Room temperature cream cheese works best for this—trust me on this one.)
Once creamy, mix in the egg, sweetener, almond flour, and vanilla extract. Stir until you have a luscious, silky filling that’s ready to take these muffins to the next level.
Pro Tip: Forgot to take the cream cheese out of the fridge? No worries—just let it sit on the counter for a bit, or pop it in the microwave for a few seconds to soften slightly.
Assemble Your Muffins
Here’s the fun part: spoon a layer of muffin batter into each cup, filling it about one-third of the way.
Top each one with a smaller scoop of cheesecake filling. Add about 1 tablespoon of the remaining pumpkin batter over the cheesecake filling.
Use a toothpick or skewer to gently swirl the pumpkin batter and cheesecake filling together. Swirl only a few times so you can still see distinct pumpkin and cheesecake layers.
Bake to Perfection
Bake the muffins for 20–25 minutes, until the pumpkin portion is set and a toothpick inserted near the edge of a muffin, away from the cheesecake center, comes out clean.
The cheesecake center may still look slightly soft when the muffins first come out of the oven.
If the tops begin browning too quickly, loosely cover the pan with foil during the final few minutes of baking.
Cool and Enjoy
Let the muffins cool in the pan for 5–10 minutes, then transfer them to a wire rack.
Enjoy them warm or at room temperature.
Tips and Variations
- Don’t use pumpkin pie filling. Make sure the can says pure pumpkin puree because pumpkin pie filling already contains sweeteners and spices.
- Adjust the spice. The recipe uses 2–3 teaspoons of pumpkin pie spice, so you can choose the amount depending on how strongly spiced you want the muffins.
- Add chocolate chips. Stir ½ cup sugar-free chocolate chips into the pumpkin batter for chocolate chip pumpkin cheesecake muffins.
- Add some crunch. Chopped pecans or walnuts can be folded into the pumpkin batter.
- Add a caramel finish. Drizzle the cooled muffins with my sugar-free caramel sauce before serving.
How to Store Pumpkin Cheesecake Muffins
Because these muffins contain a cream cheese filling, keep them refrigerated. Once they are completely cool, place them in an airtight container and store them in the refrigerator for up to four days.
For longer storage, wrap the muffins individually and place them in a freezer-safe container for up to two months. Thaw them overnight in the refrigerator before serving.
I like letting a refrigerated muffin sit at room temperature for about 10 minutes before eating. You can also warm it briefly, but the cheesecake filling will become softer.
Can I Make Mini Pumpkin Cheesecake Muffins?
Yes. You can use a mini muffin tin and follow the same layering method.
Because mini muffins are smaller, begin checking them earlier than the full-size muffins. They’re done when the pumpkin portion is set and a toothpick inserted away from the cheesecake center comes out clean.
More Keto Pumpkin Recipes
If you’re looking for more easy pumpkin recipes for fall, try these next:
- Chocolate Chip Pumpkin Muffins
- No-Bake Keto Pumpkin Cheesecake
- Keto Pumpkin Pie Cookies
- Crustless Pumpkin Pie
Keto Pumpkin Cheesecake Muffins
Description
Ingredients
For the muffin batter
- 5 large eggs room temperature
- 2 cups almond flour ultra fine, blanched
- 2 tbsp coconut flour or protein powder
- ¾ cup pumpkin puree not pumpkin pie filling
- 2-3 tsp pumpkin pie spice
- 3 tbsp heavy cream
- 3/4 cup sweetener
- 4 tbsp butter softened
- 1 1/2 tsp baking powder
- 1 tsp vanilla extract
For the cheesecake filling
- 4 oz cream cheese room temperature
- 1 large egg large
- 1/4 cup powdered sweetener
- 2 tbsp almond flour or 1 tbsp coconut flour
- 1 tsp vanilla extract
Instructions
- Prepare the pan. Preheat the oven to 350°F (180°C) and line a 12-cup muffin tin with liners.
- Make the muffin batter. In a large bowl, whisk the 5 eggs until smooth. Add the pumpkin puree, heavy cream, sweetener, softened butter, and vanilla extract. Mix until evenly combined.
- Add the almond flour, coconut flour or protein powder, pumpkin pie spice, and baking powder. Stir until combined, then set the batter aside.
- Prepare the cheesecake filling. In a medium bowl, beat the cream cheese until smooth. Add the egg, powdered sweetener, almond flour or coconut flour, and vanilla extract. Mix until smooth.
- Assemble the muffins. Add one scoop of pumpkin muffin batter to the bottom of each muffin cup.
- Add a smaller scoop of cheesecake filling on top of the pumpkin batter.
- Top each muffin with about 1 tablespoon of the remaining pumpkin batter. Use a toothpick or skewer to gently swirl the pumpkin batter and cheesecake filling together.
- Bake for 20–25 minutes, until the pumpkin portion is set and a toothpick inserted near the edge, away from the cheesecake center, comes out clean. The cheesecake center may still look slightly soft.
- Let the muffins cool in the pan for 5–10 minutes, then transfer them to a wire rack.
Nutrition information is shared to make meal planning easier. Values are estimates and can vary depending on the ingredients, brands, and serving sizes used. Learn more in my nutrition policy.
