These keto pumpkin cream cheese muffins are moist, full of pumpkin flavor, and topped with a creamy, cheesecake-like dollop, making them absolutely delicious for breakfast, snack, or dessert.

These keto pumpkin muffins are everything you love about fall, but without the carbs! They've got that warm pumpkin spice flavor and a sweet cream cheese center that tastes just like cheesecake. They’re moist, rich, and taste like the real deal. You may not even guess they’re low carb or keto-friendly!

Plus, they're super easy to make and bake in just 25 minutes. Many of the ingredients are ones you probably already have on hand like almond flour, eggs, sugar-free sweetener, cream cheese, pumpkin purée, and pumpkin pie spice.

We like to dress them up with a dollop of sugar-free whipped cream and a sprinkle of crunchy pepitas. And these little treats can be enjoyed any time of day, whether for breakfast, an afternoon snack, or an after-dinner dessert!

Key Ingredients

Almond flour: For the best texture, use blanched, super-fine almond flour. We don’t recommend coconut flour since it absorbs too much liquid and can dry out the muffins.

Pumpkin purée: Be sure to use 100% pure pumpkin with no added ingredients. Don’t confuse it with pumpkin pie filling, which contains sugar and added flavors.

Sugar-free sweetener: We use Lakanto Monk Fruit Sweetener in this recipe, but another sugar-free option such as erythritol will also work.

Eggs: We use 4 large eggs to give the muffins their moist, fluffy texture.

Pumpkin pie spice: A store-bought blend works perfectly here, but you can also make your own homemade mix if you prefer.

Cream cheese: The cream cheese filling is sweetened so it bakes into a creamy cheesecake-like center. Be sure to use block-style cream cheese, not the spreadable or whipped kind.

Preparation Steps

Prep the oven and pan: Preheat oven to 350°F. Line a muffin pan with cupcake liners.

Make the filling: In a medium bowl, beat together the cream cheese, sweetener, and vanilla extract with a mixer on medium-high speed until smooth and creamy. Set aside.

Mix dry ingredients: In a medium bowl, whisk together the almond flour, pumpkin pie spice, baking powder, and salt.

Mix wet ingredients: In a large bowl, whisk the pumpkin purée, granulated sweetener, and eggs until smooth.

Combine: Gently stir the dry ingredients into the wet ingredients until just combined. Do not overmix.

Assemble muffins: Spoon pumpkin batter into each muffin cup until about ¾ full. Add 1 teaspoon of cream cheese filling on top of the batter and lightly press it in so it settles into the surface.

Bake: Bake for 20 to 25 minutes, or until the pumpkin portion tests clean with a toothpick (the cream cheese center will remain soft). Let muffins cool in the pan for at least 10 minutes before removing. Serve as is, or top with sugar-free whipped cream and pepitas for a bakery-style finish.

Expert Tips

• Use block cream cheese: Be sure to use block-style cream cheese for the best consistency, not the spreadable or whipped kind.
• Use room-temperature eggs: They mix more evenly into the batter and help the muffins rise better. To bring eggs to room temp quickly, place them in a bowl of warm water for 5 minutes.
• Don’t overmix the batter :Overmixing can make almond flour muffins dense or tough. Gently fold the wet and dry ingredients together until just combined.
• Check for doneness early: Since ovens can vary, start checking at 20 minutes. Ours typically finish in 24 minutes. Insert a wooden toothpick into the pumpkin portion (not the cream cheese). If it comes out clean or with just a few crumbs, the muffins are done.
• Cool before serving: Let the muffins cool completely at room temperature before removing from the liners. The cream cheese center firms up as it cools, and warm muffins may crumble apart.
• Storage: Keep muffins in a covered container in the fridge for up to 5 days. For the best texture, let them come to room temperature or warm in the microwave for 10 to 15 seconds before eating.

How to Store

Since these muffins have a sweet cream cheese filling, they’re best treated like cheesecake when it comes to storage. Therefore, store in an airtight container in the refrigerator for up to 3 to 4 days. Let them come to room temp or warm them in the microwave for about 10 to 15 seconds before eating for the best texture.

More Low Carb Pumpkin Recipes

If you try this recipe, we would love to hear your feedback! Leave a comment, rate it, and tag @lowcarbsimplified on your photo of this recipe on Instagram or Facebook. We hope you enjoy this recipe as much as we do!

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