Preheat the oven to 300 degrees F (150 degrees C). Spray a 6-cup muffin pan with cooking spray and set aside.

Stir almond flour, 1 tablespoon sweetener, flax seeds, cinnamon, and salt together in a medium mixing bowl, stirring to break up any flour lumps. Add melted butter, stirring well. Distribute the crust mixture evenly into each prepared muffin cup, pressing down into the bottoms.

Bake in the preheated oven until crusts start to brown, 10 to 15 minutes. Remove from the oven and let cool for about 15 minutes.

Beat cream cheese and pumpkin together in a large bowl until smooth. Add sweetener, egg, vanilla extract, cinnamon, nutmeg, and salt; beat until well incorporated. Spoon cheesecake batter onto the cooled crusts and sprinkle pecans onto each.

Bake in the preheated oven until set, 18 to 20 minutes.

Remove from the oven, place the pan on a wire rack, and allow to cool for about 30 minutes. Place the muffin pan in the refrigerator to chill, about 30 minutes.

When ready to serve, run a knife around each cheesecake, releasing it from the muffin cup.