Prep the pan and oven: Heat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners. Lightly mist liners with cooking spray for easy release.
Whisk the dry ingredients: In a large bowl, whisk almond flour, coconut flour, sweetener, baking powder, baking soda, salt, and shredded coconut until well combined and lump-free.
Mix the wet ingredients: In a separate bowl, whisk eggs, melted butter, yogurt, lemon zest, lemon juice, and vanilla until smooth. If using coconut extract, add it now.
Combine gently: Pour wet ingredients into dry.
Stir with a spatula until just combined. The batter will be thick and scoopable. Avoid overmixing to keep the muffins tender.
Portion the batter: Divide the batter evenly among the 12 liners.
If topping with coconut flakes, sprinkle a pinch over each muffin.
Bake: Place on the center rack and bake for 18–22 minutes. Muffins are done when the tops are set, lightly golden at the edges, and a toothpick comes out mostly clean with a few moist crumbs.
Cool: Let muffins cool in the pan for 5 minutes, then move to a wire rack to finish cooling. This helps set the crumb and prevents soggy bottoms.
Optional finishing touch: For extra lemon pop, brush the warm tops with a teaspoon of fresh lemon juice mixed with a pinch of sweetener.