Preheat your oven to 400°F. Lightly grease a 12-cup muffin tin or line it with paper liners.
In a medium bowl, whisk together the flour, baking powder, baking soda, and sea salt.
In a larger bowl, combine the Greek yogurt, eggs, sugar, melted butter, milk, lemon juice, lemon zest, and vanilla extract until smooth.
Gradually fold the dry ingredients into the wet ingredients. Stir just until combined—overmixing can result in dense muffins.
Gently fold in the poppy seeds to evenly distribute them throughout the batter.
Divide the batter evenly among the muffin cups, using a ⅓-cup measuring cup for consistency. Fill each cup about three-quarters full.
Bake for 17–22 minutes, or until the muffin tops are golden and spring back when touched. A toothpick inserted into the center should come out clean.
Allow the muffins to cool in the tin for 10 minutes before transferring them to a wire rack to cool completely.
Drizzle the cooled muffins with a light lemon glaze, if desired, for an extra burst of flavor.