Preheat the oven to 400°F (200°C). Line a 12-cup muffin tin with paper liners or lightly grease each cup.
In a medium bowl, whisk together the flour, poppy seeds, baking powder, baking soda, and salt.
In a large bowl, use your fingers to rub the lemon zest into the granulated sugar until it becomes fragrant and slightly moist.
Add the eggs to the lemon-sugar mixture, whisking until smooth. Mix in the Greek yogurt, vegetable oil, lemon juice, and vanilla extract until well combined.
Gently fold the dry ingredients into the wet mixture, alternating with the milk, beginning and ending with the dry ingredients. Stir until just combined; avoid overmixing.
Divide the batter evenly among the prepared muffin cups, filling each about two-thirds full.
Bake for 18–20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the tin for 5 minutes before transferring them to a wire rack to cool completely.