These Keto Pumpkin Cheesecake Muffins are a delicious treat that combines fall flavors with a creamy cheesecake surprise inside. They’re low in carbs and super easy to make!
Perfect for breakfast or a snack, I love how you can enjoy the cozy pumpkin spice without any guilt. Plus, the cheesecake filling? Absolute bliss! 🎃🧁
Key Ingredients & Substitutions
Almond Flour: This is the base for your muffins, providing a great texture. If you’re allergic, you can substitute with sunflower seed flour, but note it may change the flavor slightly.
Coconut Flour: This helps absorb moisture. If you can’t find it, you might use more almond flour, but adjust the liquid since coconut flour is more absorbent. Start with half the amount of coconut flour and add more if needed.
Pumpkin Puree: Unsweetened pumpkin puree brings all the fall flavors. If you don’t have it, butternut squash puree works well too. Just avoid canned pumpkin pie filling, as it contains added sugars.
Erythritol: This sweetener keeps the muffins keto-friendly. You could use stevia or monk fruit sweetener as alternatives, but adjust the quantity as they vary in sweetness.
Cheese: Cream cheese is crucial for the cheesecake filling. Neufchâtel is a lighter option, and for dairy-free diets, try cashew cream as a substitute, although the texture will change slightly.
What’s the Best Way to Achieve a Creamy Cheesecake Filling?
Getting that smooth cheesecake filling requires some attention. Here’s how to do it right:
- Soften the cream cheese fully at room temperature to ensure it blends easily.
- Beat it well with an egg yolk and sweetener until fully smooth; this prevents any lumps.
- Consider using a hand mixer for a fluffier texture if you prefer, but hand whisking works too!
This creamy layer adds a gorgeous touch to the muffins, making them feel extra special!

Keto Pumpkin Cheesecake Muffins
Ingredients You’ll Need:
For the Muffins:
- 1½ cups almond flour
- 1/4 cup coconut flour
- 1 tsp baking powder
- 1 tsp pumpkin pie spice
- 1/2 tsp cinnamon
- Pinch of salt
- 2 large eggs
- 1/2 cup pumpkin puree (unsweetened)
- 1/3 cup erythritol or preferred keto sweetener
- 1/4 cup melted butter or coconut oil
- 1 tsp vanilla extract
For the Cheesecake Filling:
- 4 oz cream cheese, softened
- 1 large egg yolk
- 2 tbsp erythritol or preferred keto sweetener
- 1/2 tsp vanilla extract
For the Crumble Topping:
- 1/4 cup chopped pecans or walnuts
- 2 tbsp almond flour
- 1 tbsp erythritol
- 1/2 tsp cinnamon
- 1 tbsp melted butter
How Much Time Will You Need?
This recipe takes about 15 minutes of prep time and 25-30 minutes of baking time. After baking, allow an additional 10 minutes to cool before serving. In total, you’ll need about 1 hour to have these delicious muffins ready to enjoy!
Step-by-Step Instructions:
1. Prepping the Oven and Muffin Tin:
Start by preheating your oven to 350°F (175°C). Line a muffin tin with paper liners so your muffins don’t stick!
2. Mixing the Muffin Batter:
In a large mixing bowl, whisk together the almond flour, coconut flour, baking powder, pumpkin pie spice, cinnamon, and a pinch of salt. In another bowl, beat the eggs. Add in the pumpkin puree, erythritol, melted butter, and vanilla extract. Mix everything together until it’s nice and smooth. Combine the wet and dry mixtures, stirring gently until you have a consistent muffin batter.
3. Preparing the Cheesecake Filling:
In a small bowl, beat together the softened cream cheese, egg yolk, erythritol, and vanilla extract until you have a smooth, creamy mixture. This will be your delicious cheesecake filling!
4. Making the Crumble Topping:
In another bowl, combine the chopped nuts, almond flour, erythritol, cinnamon, and melted butter. Mix until crumbly. This will create a delightful crunchy topping for your muffins!
5. Assembling the Muffins:
Now it’s time to assemble! Fill each muffin liner with about 2 tablespoons of the pumpkin muffin batter. Then, drop in about 1 tablespoon of the cheesecake filling on top of the batter. Finally, cover the cheesecake layer gently with the rest of the muffin batter, then sprinkle the crumble topping generously over each muffin.
6. Baking the Muffins:
Place the muffin tin in the preheated oven and bake for 25-30 minutes. You’ll know they’re ready when a toothpick inserted in the base (not the cheesecake center) comes out clean and the tops are golden brown.
7. Cooling and Enjoying:
Let the muffins cool in the pan for about 10 minutes before transferring them to a wire rack to cool completely. Enjoy these delightful muffins warm or chilled! Store any leftovers in an airtight container in the refrigerator.
These Keto Pumpkin Cheesecake Muffins are perfect for a fall treat or a sweet snack that’s low on carbs. Enjoy every delicious bite!

Can I Use a Different Sweetener?
Absolutely! If you prefer a different sweetener, just be sure to check the sweetness level. Stevia or monk fruit sweeteners work well, but you may need to adjust the amount since they can be significantly sweeter than erythritol.
What if I Don’t Have Almond Flour?
If you can’t use almond flour, feel free to substitute it with sunflower seed flour for a nut-free version. However, keep in mind that the taste and texture may vary slightly.
How Should I Store the Muffins?
Store any leftovers in an airtight container in the refrigerator for up to 4 days. You can also freeze the muffins for longer storage; just make sure they’re wrapped well to prevent freezer burn!
Can I Make These Muffins Ahead of Time?
Yes, you can prepare the muffin batter and cheesecake filling ahead of time! Store them separately in the fridge for up to 2 days. Just assemble and bake when you’re ready to enjoy them!


