Keto Pumpkin Cream Cheese Muffins Recipe

Dessert

March 10, 2026

When the air turns crisp and the leaves start to fall, my kitchen is filled with the warm, comforting aroma of pumpkin spice. These Keto Pumpkin Cream Cheese Muffins are the ultimate autumn indulgence, without any of the guilt. Imagine a tender, spiced pumpkin muffin with a delightful surprise inside: a rich, tangy cream cheese filling. They’re perfectly moist, incredibly easy to whip up, and destined to become your new favorite low-carb treat for cozy mornings or afternoon coffee breaks.

Ingredients

• For the Cream Cheese Filling
• Cream cheese, softened: 6 oz / 170 g
• Powdered Swerve sweetener: 3 tbsp / 36 g
• Heavy cream: 1 tbsp / 15 ml
• Vanilla extract: ½ tsp / 2.5 ml
• For the Pumpkin Muffins
• Almond flour: 2 cups / 224 g
• Swerve sweetener: ½ cup / 96 g
• Baking powder: 2 tsp / 8 g
• Unflavored whey protein powder: ¼ cup / 24 g
• Pumpkin pie spice: 2 tsp / 6 g
• Salt: ½ tsp / 3 g
• Large eggs: 2
• Pumpkin puree: ½ cup / 122 g
• Butter, melted: ¼ cup / 57 g
• Unsweetened almond milk: ¼ cup / 60 ml
• Vanilla extract: ½ tsp / 2.5 ml

Instructions

1. Preheat your oven to 325°F (165°C). Line a 12-cup muffin tin with silicone or parchment paper liners.
2. In a medium bowl, prepare the filling by combining the softened cream cheese, powdered Swerve, heavy cream, and vanilla. Beat with an electric mixer until smooth and creamy. Set aside.
3. In a large bowl, whisk together all the dry muffin : almond flour, Swerve sweetener, baking powder, whey protein powder, pumpkin pie spice, and salt.
4. In a separate bowl, whisk the eggs, then mix in the pumpkin puree, melted butter, unsweetened almond milk, and vanilla extract until well combined.
5. Pour the wet into the bowl with the dry . Stir gently until just combined—be careful not to overmix.
6. Spoon about a tablespoon of batter into the bottom of each muffin liner. Use the back of the spoon to create a small well in the center.
7. Drop a heaping teaspoon of the cream cheese filling into each well. Top with the remaining pumpkin batter, making sure the filling is completely covered.
8. Bake for 22-25 minutes, or until a toothpick inserted into the muffin part (avoiding the filling) comes out clean.
9. Let the muffins cool in the pan for 15 minutes before carefully transferring them to a wire rack to cool completely. This step is crucial to prevent them from falling apart.

Nutritional Information

• Serving Yields: 12 muffins
• Net Carbs: 3.8 g
• Total Fats: 18.4 g
• Protein: 7.5 g
• Calories: 221

Pro Tips

• For a smooth, lump-free cream cheese filling, ensure your cream cheese and eggs are at room temperature before you begin mixing.
• When combining the wet and dry muffin , mix only until they are just incorporated. Overmixing can develop the gluten in the flour, leading to dense, tough muffins.
• Out of pumpkin pie spice? Make your own by mixing 1 tsp cinnamon, ½ tsp ground ginger, and ¼ tsp ground cloves.
• Store these muffins in an airtight container in the refrigerator for up to 5 days. The cream cheese filling means they should not be left at room temperature for extended periods.

FAQ

Q: Can I use coconut flour instead of almond flour in this recipe
A: We do not recommend substituting coconut flour for almond flour in this recipe. Coconut flour is much more absorbent and would require significant adjustments to the wet ingredients. For the best texture and results, please use almond flour as listed.

Q: Is the whey protein powder necessary for these muffins
A: The unflavored whey protein powder helps give the muffins a better structure and a lighter, fluffier texture. You can omit it if you don’t have it, but your muffins may turn out slightly denser.

Q: How should I store these keto pumpkin muffins
A: Due to the cream cheese filling, these muffins must be stored in an airtight container in the refrigerator. They will stay fresh for up to 5 days.

Q: Can I freeze these pumpkin cream cheese muffins
A: Yes, these muffins freeze beautifully. Allow them to cool completely, then place them in a freezer-safe bag or container. They can be frozen for up to 3 months. Thaw in the refrigerator or at room temperature before enjoying.

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