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Keto Pumpkin Muffins with Cream Cheese Filling
As the crisp autumn air sets in, cravings for warm, comforting treats often emerge. Have you ever found yourself wishing for an indulgent yet healthy snack to enjoy with your afternoon coffee? Enter Keto Pumpkin Muffins with Cream Cheese Filling! These delightful muffins marry the spiced goodness of pumpkin with a creamy, luscious center that will please even the pickiest eaters. They are not only low in carbs but also incredibly easy to whip up, making them a perfect addition to your fall baking repertoire. Here’s everything you need to know to make it tonight. You may also find Blueberry Lemon Sourdough With Cream Cheese Swirl useful.

Why You’ll Love This Recipe
- Irresistibly moist: The cream cheese filling keeps these muffins beautifully moist and rich.
- Keto-friendly: Low in carbs and sugar, perfect for those following a ketogenic lifestyle.
- Quick to prepare: Ready in about 30 minutes, so you can enjoy them almost immediately.
- Kid-approved: Even non-keto munchers will love the sweet pumpkin flavor combined with the creamy filling.
- Batch-friendly: Great for meal prep or freezing, so you can have snacks ready whenever you need them.
Ingredients
For the Muffins
- 1 cup almond flour
- 1/2 cup coconut flour
- 1/2 cup pumpkin puree (fresh or canned)
- 1/2 cup sugar-free sweetener (like erythritol or stevia)
- 3 large eggs
- 1 tsp vanilla extract
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp cinnamon
- 1/4 tsp nutmeg
- 1/4 cup cream cheese (softened)
- 1 tbsp butter (melted)
- 1/4 tsp salt
For the Cream Cheese Filling
- 1/4 cup cream cheese (softened)
- 2 tbsp sugar-free sweetener
Make sure your cream cheese is softened before beginning this recipe for the best texture. You can pair these muffins with some delicious pumpkin cream cheese muffins for a more festive spread!

Step-by-Step Instructions
- Preheat the oven to 350°F (175°C) and line a muffin tin with paper liners.
- Mix the dry ingredients: In a bowl, combine almond flour, coconut flour, baking powder, baking soda, spices, and salt.
- Create the pumpkin mixture: In another bowl, mix pumpkin puree, sugar-free sweetener, eggs, vanilla extract, and melted butter until smooth and fully combined.
- Combine the mixtures: Gradually add the dry ingredients to the pumpkin mixture, stirring until just combined. Don’t overmix to keep them fluffy!
- Prepare the cream cheese filling: In a separate bowl, soften the cream cheese and mix with a little sweetener until smooth.
- Fill the muffin liners: Fill each muffin liner halfway with the batter, add a small dollop of the cream cheese filling in the center, and then top with more batter.
- Bake to perfection: Bake for 20-25 minutes, or until a toothpick inserted into the muffin comes out clean.
- Cool and enjoy: Let the muffins cool before serving to allow the flavors to meld together. Enjoy your keto muffins!
Pro Tips & Variations
- Tip for fluffy muffins: Be gentle when mixing and don’t overwork the batter, as this can lead to denser muffins.
- Use room temperature ingredients: Allow the eggs and cream cheese to sit at room temperature for at least 30 minutes before use for a smooth batter.
- Easy swaps: If you’re looking for dairy-free options, you can replace cream cheese with a non-dairy cream cheese alternative.
- Try different flavors: You can add in dark chocolate chips or nuts for extra texture and flavor.
Storage & Reheating
- Fridge: Store muffins in an airtight container in the refrigerator for up to a week.
- Freezer: Freeze the muffins individually in a zip-top bag for up to three months. Thaw at room temperature or microwave for a few seconds until warmed.
- Reheating: To enjoy, simply warm them in the microwave or oven to get that fresh-baked taste back.
FAQ
-
Can I use different types of flour?
- Yes, you can experiment with other nut flours, but the texture may vary slightly.
-
Can I make these muffins ahead of time?
- Absolutely! These muffins keep well in the fridge or freezer, making them great for meal prep.
-
What can I serve with these muffins?
- They pair wonderfully with coffee or a warm cup of tea for a cozy afternoon treat.
-
Can I substitute the sweetener?
- Yes, feel free to use your preferred sweetener, adjusting the quantity to taste.
-
How many muffins does this recipe make?
- This recipe typically yields about 12 muffins.
-
Can I add chocolate chips?
- Certainly! Dark chocolate chips can be a delicious addition to the batter.
Conclusion
Keto Pumpkin Muffins with Cream Cheese Filling are not only simple to make, but they also embody the flavors of fall while adhering to a healthy diet. If you’re looking for more variations, check out these Keto Pumpkin Cream Cheese Muffins or explore the delicious Keto Pumpkin Muffins with a cheesecake center. Enjoy baking, and don’t forget to leave a comment with your thoughts! These muffins are bound to become a favorite in your house!

Keto Pumpkin Muffins with Cream Cheese Filling
Ingredients
For the Muffins
- 1 cup almond flour
- 1/2 cup coconut flour
- 1/2 cup pumpkin puree (fresh or canned)
- 1/2 cup sugar-free sweetener (like erythritol or stevia)
- 3 large eggs
- 1 tsp vanilla extract
- 1 tsp baking powder
- 1/2 tsp baking soda
- 1/2 tsp cinnamon
- 1/4 tsp nutmeg
- 1/4 cup cream cheese (softened)
- 1 tbsp butter (melted)
- 1/4 tsp salt
For the Cream Cheese Filling
- 1/4 cup cream cheese (softened)
- 2 tbsp sugar-free sweetener
Instructions
Preparation
- Preheat the oven to 350°F (175°C) and line a muffin tin with paper liners.
- In a bowl, combine almond flour, coconut flour, baking powder, baking soda, spices, and salt.
- In another bowl, mix pumpkin puree, sugar-free sweetener, eggs, vanilla extract, and melted butter until smooth and fully combined.
- Gradually add the dry ingredients to the pumpkin mixture, stirring until just combined. Don’t overmix to keep them fluffy!
- In a separate bowl, soften the cream cheese and mix with a little sweetener until smooth.
- Fill each muffin liner halfway with the batter, add a small dollop of the cream cheese filling in the center, and then top with more batter.
Baking
- Bake for 20-25 minutes, or until a toothpick inserted into the muffin comes out clean.
- Let the muffins cool before serving to allow the flavors to meld together.