Heat oven to 350°F. Line a muffin pan with cupcake liners. Spray the liners with nonstick spray. Set aside.
Combine almond flour, baking powder, and salt. whisk until ingredients are well combined.
Whisk together in a large bowl the sugar, eggs, lemon zest and juice, and vanilla extract. Add to the dry ingredients and whisk until completely incorporated.
Divide batter evenly between the muffin liners. Each should be about ¾ full with 3 heaping tablespoons of batter in each.
Bake for 18 minutes, until the internal temperature registers 203–205°F.
Remove from the oven and let cool in the pan for 10 minutes. Remove cupcakes to a cooling rack and let cool completely before frosting.
Meanwhile, beat the cream cheese, sugar, yogurt, vanilla, and lemon extract in a mixing bowl until smooth.
Place about 2 tablespoons of frosting onto the cooled cupcake. Use a small offset spatula to spread the frosting to the edge. While pressing down on the frosting slightly, move the spatula in a spiral pattern to create a pretty swoop! Serve immediately.
(You can also do as I did here and decorate with a piping bag and dragees!)