Prep the pan. Heat the oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners and lightly mist with oil for easy release.
Mix dry ingredients. In a large bowl, whisk almond flour, coconut flour, erythritol, baking powder, baking soda, and salt until no lumps remain.
Whisk wet ingredients. In another bowl, whisk eggs, almond milk, melted butter, Greek yogurt, and vanilla until smooth.
If using almond extract, add it here.
Combine gently. Add the wet mixture to the dry and stir with a spatula until just combined. The batter should be thick but scoopable. If it seems too thick, add 1–2 tablespoons more almond milk.
Fill the liners. Divide batter evenly among the 12 cups, filling each about 3/4 full.
Tap the pan gently to level tops.
Bake. Bake for 18–22 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs. Do not overbake.
Cool completely. Let cupcakes cool in the pan for 5 minutes, then transfer to a rack. Cool fully before frosting.
Optional frosting. Beat 6 oz cream cheese, 3 tbsp softened butter, 1/3 cup powdered keto sweetener, 1 tsp vanilla, and a pinch of salt until fluffy.
Thin with 1–2 tsp almond milk if needed. Pipe or spread onto cooled cupcakes.