These Keto Pumpkin Cheesecake Muffins are soft and tender with plenty of warm pumpkin spice flavor and a creamy cheesecake swirl in every muffin. They’re naturally gluten-free, low-carb, and made without added sugar, making them a delicious fall dessert, snack, or breakfast treat.
Prepare the pan. Preheat the oven to 350°F (180°C) and line a 12-cup muffin tin with liners.
Make the muffin batter. In a large bowl, whisk the 5 eggs until smooth. Add the pumpkin puree, heavy cream, sweetener, softened butter, and vanilla extract. Mix until evenly combined.
Add the almond flour, coconut flour or protein powder, pumpkin pie spice, and baking powder. Stir until combined, then set the batter aside.
Prepare the cheesecake filling. In a medium bowl, beat the cream cheese until smooth. Add the egg, powdered sweetener, almond flour or coconut flour, and vanilla extract. Mix until smooth.
Assemble the muffins. Add one scoop of pumpkin muffin batter to the bottom of each muffin cup.
Add a smaller scoop of cheesecake filling on top of the pumpkin batter.
Top each muffin with about 1 tablespoon of the remaining pumpkin batter. Use a toothpick or skewer to gently swirl the pumpkin batter and cheesecake filling together.
Bake for 20–25 minutes, until the pumpkin portion is set and a toothpick inserted near the edge, away from the cheesecake center, comes out clean. The cheesecake center may still look slightly soft.
Let the muffins cool in the pan for 5–10 minutes, then transfer them to a wire rack.