Keto Pumpkin Muffins – Soft, Low-Carb with Cream Cheese Filling

Keto Pumpkin Muffins are soft, warmly spiced pumpkin muffins with a creamy cheesecake-style center and a tender almond flour crumb. They are lightly sweet, rich without feeling heavy, and perfect when you want a cozy fall-style treat that fits a lower-carb baking style.

These muffins have a lot going for them. The pumpkin keeps them moist, the spice blend gives them that classic bakery-style fall flavor, and the cream cheese filling adds a smooth surprise in the middle.

They are especially nice for breakfast, snack time, or a make-ahead treat to keep in the fridge. If you enjoy pumpkin desserts with a soft texture and a creamy center, this is one to keep on repeat.

Why You’ll Love This Recipe

• Soft pumpkin muffins with a creamy cheesecake filling
• Cozy pumpkin spice flavor in every bite
• Lower-carb and made with almond flour
• Great for breakfast, snack time, or dessert
• Easy to make ahead and store in the fridge

Ingredients

Candy base

• 2 cups almond flour (210 g)
• 1/2 cup Swerve Sweetener (91 g)
• 1/4 cup unflavored whey protein powder or egg white protein (27 g)
• 2 teaspoons baking powder
• 2 teaspoons pumpkin pie spice
• 1/2 teaspoon salt
• 2 large eggs
• 1/2 cup pumpkin puree (about 123 g)
• 1/4 cup butter, melted (about 57 g)
• 1/4 cup water (about 60 ml)
• 1/2 teaspoon vanilla extract

Finish

• 6 oz cream cheese, softened (170 g)
• 3 tablespoons powdered Swerve Sweetener
• 1 tablespoon heavy cream
• 1/2 teaspoon vanilla

Ingredient Notes & Substitutions

• Almond flour gives these muffins their tender, moist texture. Use fine blanched almond flour, not almond meal, for the best crumb.
• Swerve keeps the muffins sugar-free while still giving them sweetness. Another similar granulated keto baking sweetener may work, but texture can vary.
• Whey protein powder helps with structure. Egg white protein is the closest swap if you do not want whey.
• Pumpkin puree should be plain pumpkin, not pumpkin pie filling.
• Melted butter adds richness, but let it cool slightly before mixing it in.
• Full-fat cream cheese gives the filling the best creamy texture.
• Pumpkin pie spice works well as written, but you can use 1 teaspoon cinnamon, 1/2 teaspoon ginger, and 1/4 teaspoon cloves if needed.

How to Make Keto Pumpkin Muffins

• Preheat the oven to 350°F and line a muffin pan with paper liners.
• In a large bowl, whisk together the almond flour, Swerve Sweetener, whey protein powder, baking powder, pumpkin pie spice, and salt.
• Add the eggs, pumpkin puree, melted butter, water, and vanilla extract. Stir until the batter is smooth and evenly combined.

• In a small bowl, mix the softened cream cheese, powdered Swerve Sweetener, heavy cream, and vanilla until smooth. Set aside.

• Divide part of the muffin batter among the lined muffin cups.
• Add a spoonful of the cream cheese filling to the center of each muffin.
• Top with the remaining muffin batter so the filling is mostly covered.
• Bake until the tops are set and lightly golden and a tester around the muffin edge comes out clean, about 20 to 24 minutes.

• Cool in the pan for several minutes, then transfer to a wire rack to cool completely.

Expert Tips

• Use softened cream cheese so the filling mixes up completely smooth.
• Do not overfill the muffin cups because the muffins rise a bit as they bake.
• If the batter feels thick, that is normal for almond flour muffins.
• Spoon the filling into the center rather than spreading it to the edges for a cleaner look.
• Let the muffins cool before serving so the filling can set properly.
• Bake until the tops are just set; overbaking can dry out almond flour muffins.
• Store them chilled for the best texture and cleanest center.
• Add a pinch more pumpkin pie spice if you want a bolder fall flavor.

Storage & Freezing

• Store Keto Pumpkin Muffins in an airtight container in the refrigerator for up to 5 days.
• Because of the cream cheese filling, these muffins should be kept chilled. Let them sit at room temperature for a few minutes before serving if you want a softer texture.
• To freeze, place the cooled muffins in a freezer-safe container and freeze for up to 2 months.
• Thaw overnight in the refrigerator, then enjoy chilled or bring to room temperature for a few minutes before serving.

Variations

• Add chopped pecans or walnuts to the muffin batter
• Use extra cinnamon for a warmer spice profile
• Add a little orange zest to the filling for a fresh twist
• Make them mini for bite-size keto pumpkin muffins
• Top with a few sugar-free chocolate chips before baking

FAQs

More Recipes You Will Like :

• Mini Cinnamon Muffins
• Easy Roasted Pumpkin Recipe (Crispy, Healthy & Full of Flavor)
• Pumpkin Dessert Recipe (Easy Oven-Baked with Walnuts)
• Pumpkin Spice Baked Oatmeal – Healthy Make-Ahead Breakfas

Estimated reading time: 7 minutes