Prep the oven and pan: Preheat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners. Lightly spritz the liners if they’re not nonstick.
Mix dry ingredients: In a large bowl, whisk 2 cups fine almond flour, 1/2 cup granulated keto sweetener, 2 teaspoons baking powder, and 1/4 teaspoon salt until evenly combined and lump-free.
Whisk wet ingredients: In a separate bowl, whisk 3 large eggs, 1/3 cup melted butter (or coconut oil), 1/3 cup unsweetened almond milk or heavy cream, and 2 teaspoons vanilla extract.
Combine batter: Pour the wet ingredients into the dry. Stir with a spatula until just combined.
The batter will be thick but scoopable. If adding mix-ins, fold them in now.
Portion: Divide the batter evenly among the liners, filling each about 3/4 full. Smooth the tops lightly with a spoon.
Bake: Bake for 18–22 minutes, or until the tops are set and a toothpick comes out mostly clean with a few moist crumbs.
Cool: Let cupcakes cool in the pan for 5 minutes, then transfer to a wire rack to cool completely before frosting.
Optional frosting: Beat 6 ounces softened cream cheese, 4 tablespoons softened butter, 1/3–1/2 cup powdered keto sweetener (to taste), 1 teaspoon vanilla, and 1–2 tablespoons cream until smooth and fluffy.
Pipe or spread onto cooled cupcakes.