Set the oven rack to the center position and preheat to 350°F before preparing a twelve-cup muffin tin with non-stick liners or oil spray. Proper preheating guarantees an immediate leavening rise when the batter hits the heat.

Beat the softened butter and two-thirds cup of sweetener in a wide mixing bowl until the mixture looks pale and aerated. Creaming builds tiny air pockets that lighten the naturally dense low-carb crumb.

Incorporate the eggs one by one, mixing thoroughly after each addition. Gradual addition prevents the emulsion from breaking and maintains a cohesive wet base.

Whisk the pumpkin puree and vanilla extract directly into the wet ingredients until uniform in color. The mixture will look glossy and turn a rich golden orange.

Whisk together the almond flour, coconut flour, baking powder, pumpkin spice, and salt in a second bowl, pressing out any dense almond meal clumps. Breaking up lumps ensures even spice distribution and uniform leavening throughout the batter.

Fold the dry flour mixture into the pumpkin base until fully combined, then portion the thick batter equally among the prepared muffin cups. Low-carb muffin batter is substantially thicker than traditional wheat batter and should mound slightly in each cup.

Blend the softened cream cheese with the remaining tablespoon of sweetener in a small bowl, drop a generous tablespoon over each muffin, and drag a toothpick through the top to create a marble pattern. A gentle figure-eight motion distributes the cheesecake layer without burying it completely into the batter.

Bake for 20 to 25 minutes until the exposed pumpkin crumb springs back when lightly pressed and a toothpick inserted into the cake portion emerges clean. Avoid testing the soft cheese center so you do not mistake melted cream cheese for uncooked cake batter.