Preheat your oven to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease each cup.
In a large bowl, whisk together the all-purpose flour, almond flour, protein powder, baking powder, baking soda, salt, poppy seeds, and lemon zest. Break up any clumps.
In a separate bowl, whisk the eggs, Greek yogurt, oil, milk, sugar, lemon juice, and vanilla until smooth and well combined.
Pour the wet mixture into the dry ingredients. Stir with a spatula just until no dry spots remain. Do not overmix—a few small lumps are fine.
Divide the batter evenly among the muffin cups, filling each about 3/4 full.
Bake for 16–20 minutes, or until the tops are set and a toothpick inserted in the center comes out with a few moist crumbs.
Cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
For the glaze, whisk powdered sugar with lemon juice to a pourable consistency.
Drizzle over cooled muffins. Let it set for 10 minutes before serving.