Preheat and prep: Heat your oven to 350°F (175°C). Line a 12-cup muffin pan with liners.
Lightly mist with nonstick spray to prevent sticking.
Mix dry ingredients: In a large bowl, whisk 2 cups almond flour, 2 tablespoons coconut flour, 1 tablespoon baking powder, 1/2 teaspoon xanthan gum, 1 teaspoon pumpkin pie spice, and 1/4 teaspoon salt until well combined and lump-free.
Whisk wet ingredients: In another bowl, whisk 3 large eggs, 3/4 cup pumpkin purée, 1/2 cup granulated keto sweetener, 1/3 cup melted butter, 1/3 cup unsweetened almond milk, and 1 teaspoon vanilla. The mixture should be smooth and glossy.
Combine: Pour wet ingredients into dry. Stir gently with a spatula until just combined.
The batter will be thicker than classic cupcake batter but should be scoopable. If it seems too stiff, add 1–2 tablespoons more almond milk.
Fill the liners: Divide the batter evenly among the 12 liners, filling each about 3/4 full. Smooth the tops slightly with the back of a spoon for even domes.
Bake: Bake for 18–22 minutes, until the tops spring back lightly and a toothpick comes out clean or with a few moist crumbs.
Avoid overbaking to keep them tender.
Cool completely: Let cupcakes cool in the pan for 5 minutes, then transfer to a rack to cool fully before frosting. This prevents melting and sliding.
Make the frosting: Beat 6 ounces softened cream cheese and 1/2 cup softened butter until creamy and fluffy, about 2–3 minutes. Add 1 1/4 cups powdered keto sweetener, 1 teaspoon vanilla, 1 teaspoon ground cinnamon, and a pinch of salt.
Beat until smooth and light. If too thick, add 1–2 teaspoons almond milk. If too loose, add a bit more powdered sweetener.
Frost: Spoon or pipe the frosting onto cooled cupcakes.
For a bakery look, use a large round or star tip. Dust with a light sprinkle of cinnamon if you like.
Set and serve: Chill frosted cupcakes for 15–20 minutes to help the frosting set, then serve at room temperature for the best texture.