First, preheat your oven to 375°F (190°C) to ensure it’s ready when your batter is mixed. Prepare a 12-cup muffin tin by lining it with paper cups or lightly greasing it with butter or non-stick spray. This step prevents sticking and makes cleanup much easier.
In a large bowl, whisk together the all-purpose flour, poppy seeds, baking powder, baking soda, and salt. Mixing the dry ingredients thoroughly ensures that the leavening agents are evenly distributed, which will help your muffins rise uniformly and have a consistent texture throughout.
In a separate medium-sized bowl, whisk the granulated sugar with the slightly cooled melted butter. Add the eggs, whole milk, fresh lemon juice, lemon zest, and vanilla extract. Continue whisking until the mixture is smooth, well-combined, and slightly pale in color.
Pour the wet ingredient mixture into the bowl with the dry ingredients. Use a spatula to gently fold them together until they are just combined. Be careful not to overmix the batter, as this can develop the gluten in the flour and result in tough, rubbery muffins.
Divide the batter evenly among the 12 prepared muffin cups, filling each one about two-thirds full. Bake for 16 to 20 minutes. You’ll know they’re done when a toothpick inserted into the center of a muffin comes out clean or with a few moist crumbs attached.
If you’re adding the glaze, wait until the muffins have cooled completely. In a small bowl, whisk together the powdered sugar and lemon juice until you have a smooth, pourable consistency. Drizzle the glaze over the tops of the muffins and let it set before serving.