Preheat oven to 400 degrees (F). Line a 12 cup muffin tin with paper liners; set aside.: When you step into the kitchen you should immediately notice warmth radiating from the preheated oven and the faint metallic scent of a hot pan. Getting the oven temperature right is crucial because it jump starts the rise, creating the characteristic domed tops and a light crust. A common mistake is to skip preheating, which can lead to flat muffins or uneven bake. If using a dark or glass pan, reduce the temperature by about 25 degrees to prevent overbrowning.
In a large bowl, sift together 3 cups of the flour, baking powder, and salt; set aside.: You will sense a clean, floury aroma as you sift, and the sifted flour will feel light and airy between your fingers. Sifting distributes the baking powder and salt evenly, which helps each muffin rise consistently. Not sifting can leave pockets of leavening, causing odd textures. Use a whisk if you don't have a sifter to achieve a similar effect.
In a large bowl using a handheld electric mixer, or in the bowl of a stand mixer fitted with the paddle attachment, combine the butter, sugar, lemon zest, and vanilla extract; beat on medium speed until light and fluffy, about 3 minutes.: As you beat, you'll notice the mixture lighten in color and become airy, with a soft, whipped texture that holds a ribbon when lifted. This aeration is what gives your muffins lift and tenderness. Overbeating after adding flour can make the crumb tough, so stop once the mixture appears pale and voluminous.
Add in the eggs, one at a time, beating well after each addition and scraping down the sides of the bowl as needed.: The batter will smell richer and slightly eggy, and you should see it smooth out and become more cohesive with each egg incorporated. Scraping down ensures no streaks of unmixed butter remain, which could create uneven pockets. A pitfall here is adding cold eggs which can seize the butter, so use room temperature eggs for best results.
Turn mixer off and set batter aside for a moment. In a spouted bowl or measuring cup add the sour cream and lemon juice; whisk well to combine and set aside. In a separate bowl combine add the blueberries and remaining flour; toss well to coat the berries in the flour.: The sour cream and lemon juice will smell tangy and fresh, and whisking them creates a smooth, creamy mixture that brightens the batter. Coating the blueberries in the remaining flour helps them stay suspended in the batter, reducing sinking during baking. A common slip is skipping the coating step, which often results in berries clustered at the bottom of the muffins.
With the mixer speed on low, alternate adding the flour mixture and the sour cream mixture, beginning and ending with flour. Be sure not to over mix here. Fold the blueberries and poppy seeds into the batter, mixing just until evenly combined.: You should hear a quieter, thicker sound as you fold, and visually the batter will move slowly from side to side. Alternating keeps the batter balanced in moisture and structure, producing a tender interior. Overmixing at this point develops gluten and yields a dense muffin, so stop when you see no streaks of flour. When folding in the blueberries , use gentle motions to avoid bursting them.
Divide the batter evenly among prepared muffin tins.: As you portion the batter, it should fall in heavy spoonfuls that hold shape, with small visible flecks of zest and poppy seeds. Using an ice cream scoop helps ensure consistent sizes so they bake uniformly. Filling liners too full can cause overflow and uneven domes, while underfilling results in small, flatter muffins.
Bake for 25 to 27 minutes, or until the tops are lightly golden brown and a toothpick inserted in the middle comes out clean, or with a just a few moist crumbs attached. Cool muffins 10 minutes in the pan before transferring to a cooling rack.: While baking you will notice a warm lemon scent filling the kitchen and a gentle crackle as the tops set. Look for a pale golden color and that classic springy touch when pressed. Cooling briefly in the pan helps them set so they won’t collapse when moved. Removing them too quickly can cause tearing, and leaving them too long in the pan can trap steam and make the bottoms soggy.
In a medium mixing bowl combine the confectioners' sugar, lemon juice, zest, and milk; whisk until smooth, adding more milk as needed to reach desired consistency. Drizzle over the muffins right before serving.: The glaze will smell intensely of lemon and look glossy as you whisk. A thin ribbon of glaze should fall in a continuous stream when drizzled, settling into the nooks on top of each muffin. Glazing while muffins are warm helps the glaze set with a slight soak in, but glazing them too hot can make the glaze run off entirely. Aim for warm, not piping hot, for the best finish.