These Keto Pumpkin Cheesecake Muffins are a tasty treat without the extra carbs! They blend pumpkin goodness with creamy cheesecake for a delightful bite.
They’re perfect for breakfast or a snack, and honestly, they make my kitchen smell incredible! I love sneaking a few while they cool down. Yum! 😋
Key Ingredients & Substitutions
Pumpkin Puree: Using real pumpkin puree brings the best flavor. If you can’t find it, cooked and mashed fresh pumpkin works well too! Just avoid pumpkin pie filling as it’s sweetened and spiced.
Almond Flour: A staple for keto baking, almond flour gives muffins a nice texture. If nut-free, try sunflower seed flour, but watch for color changes in baking!
Coconut Flour: This flour absorbs a lot of moisture, so you can’t substitute it one-for-one. If you’re short on it, use extra almond flour, but reduce the liquid ingredients slightly.
Erythritol: This is my go-to keto sweetener! If you prefer, feel free to substitute with monk fruit sweetener or stevia, adjusting to taste.
Cream Cheese: For the cheesecake swirl, regular cream cheese is great, but you can also use vegan cream cheese or Greek yogurt for a lower fat option.
How Do You Get the Perfect Cheesecake Swirl?
Creating the cheesecake swirl is a fun step! Easily elevate your muffins. Here’s how to do it right:
- Mix the cream cheese until super smooth. No lumps means a better swirl!
- After adding muffin batter to the tin, top each with a dollop of cream cheese mixture. Keep it in the center to swirl!
- Use a toothpick or knife to gently swirl. Don’t mix it in too much—keep it on top for that beautiful effect!
This technique gives your muffins a gorgeous look and a delicious creamy bite!

Keto Pumpkin Cheesecake Muffins
Ingredients You’ll Need:
For The Muffins:
- 1 cup pumpkin puree (not pumpkin pie filling)
- 3 large eggs
- 1/2 cup almond flour
- 1/4 cup coconut flour
- 1/2 cup erythritol or preferred keto sweetener, divided
- 1/4 cup melted butter or coconut oil
- 1 teaspoon baking powder
- 1 teaspoon pumpkin pie spice
- 1/2 teaspoon vanilla extract
- 1/4 teaspoon salt
For The Cheesecake Swirl:
- 4 oz cream cheese, softened
- 2 tablespoons erythritol or preferred keto sweetener
- 1/2 teaspoon vanilla extract
How Much Time Will You Need?
This recipe takes about 15 minutes to prepare and 22-25 minutes to bake, plus some time to cool. In total, you’ll be enjoying these delicious muffins in around 45 minutes! Quick and delightful!
Step-by-Step Instructions:
1. Preheat and Prepare:
Start by preheating your oven to 350°F (175°C). While the oven is heating, line a muffin tin with paper liners to make for easy clean-up!
2. Mix the Pumpkin Batter:
In a mixing bowl, combine the pumpkin puree, eggs, melted butter (or coconut oil), vanilla extract, and half of the erythritol (1/4 cup). Stir everything together until it’s smooth and well combined. This is the delicious base of your muffins!
3. Combine Dry Ingredients:
In another bowl, whisk together the almond flour, coconut flour, baking powder, pumpkin pie spice, and salt. Mix it well to ensure everything is evenly combined.
4. Bring It All Together:
Now, slowly add the dry ingredients to the wet pumpkin mixture. Stir until everything is fully combined—no lumps allowed! The batter will be thick and fragrant!
5. Prepare the Cheesecake Mixture:
In a separate bowl, mix the softened cream cheese with the remaining erythritol and half a teaspoon of vanilla extract. Beat this mixture until it’s creamy and smooth—this will create a lovely swirl in your muffins!
6. Fill the Muffin Tin:
Spoon the pumpkin muffin batter evenly into each muffin liner, filling them about three-quarters full. This gives them room to rise without overflowing.
7. Add the Cheesecake Swirl:
Now, take a spoonful of the creamy cheesecake mixture and place it on top of each muffin batter. Use a toothpick or knife to gently swirl it into the batter without completely mixing it in. You want some cheesecake goodness to peek through!
8. Bake:
Place the muffin tin in the preheated oven and bake for 22-25 minutes. Check doneness by inserting a toothpick into the muffin—make sure to avoid the cream cheese area. If it comes out clean, your muffins are ready!
9. Cool:
Once baked, remove the muffins from the oven and let them cool in the tin for about 10 minutes. After that, carefully transfer them to a wire rack to cool completely.
10. Enjoy Your Muffins:
These muffins are delightful when warm but can also be enjoyed chilled. Perfect for a keto-friendly breakfast or a delicious snack anytime!

Can I Use a Different Sweetener Besides Erythritol?
Absolutely! You can substitute erythritol with monk fruit sweetener or stevia. Just be sure to adjust the quantity according to your taste, as some sweeteners are sweeter than others.
Can I Make These Muffins Dairy-Free?
Yes! To make the muffins dairy-free, substitute the cream cheese with a dairy-free cream cheese alternative or use Greek yogurt. For the melted butter, use coconut oil or avocado oil instead!
How Should I Store Leftover Muffins?
Store leftover muffins in an airtight container at room temperature for up to 3 days. If you want them to last longer, keep them in the fridge for up to a week. You can also freeze them for up to 3 months—just thaw before enjoying!
Can I Add Other Ingredients Like Nuts or Chocolate Chips?
Definitely! Feel free to add some chopped nuts, sugar-free chocolate chips, or even dried cranberries to the batter for added texture and flavor. Just be mindful of the overall carb count if you’re keeping it strict on keto!


