Prep your pan and oven. Line a 12-cup muffin pan with paper liners.
Preheat the oven to 350°F (175°C).
Mix the dry ingredients. In a large bowl, whisk almond flour, coconut flour, granulated sweetener, baking powder, and salt until evenly combined.
Whisk the wet ingredients. In a separate bowl, whisk eggs, melted butter, yogurt, lemon zest, lemon juice, and vanilla until smooth.
Combine gently. Pour the wet mixture into the dry. Stir with a spatula until just combined. The batter will be thick but scoopable.
If it seems too thick, add 1–2 tablespoons of almond milk or water.
Fill the liners. Divide the batter evenly among the 12 liners, about 3/4 full. Smooth the tops with the back of a spoon.
Bake. Bake for 18–22 minutes, or until the tops spring back and a toothpick comes out clean or with a few moist crumbs.
Cool completely. Let cupcakes cool in the pan for 5 minutes, then transfer to a rack to cool fully before frosting.
Make the frosting. Beat cream cheese and butter until creamy. Add powdered sweetener, lemon juice, zest, vanilla, and a pinch of salt.
Beat until fluffy. Adjust sweetness and lemon to taste.
Frost and finish. Spread or pipe frosting onto cooled cupcakes. Garnish with extra zest or a thin lemon slice if you like.