Preheat your oven to 350°F (175°C) to ensure even baking.
Line a muffin tin with paper liners or grease it lightly with cooking spray.
In a large mixing bowl, combine 3 cups of all-purpose flour, 1 tablespoon of baking powder, 1/4 teaspoon of baking soda, and 1/4 teaspoon of salt. Whisk until well blended.
In another bowl, whisk together 1 cup of granulated sugar and 2 teaspoons of lemon zest until fragrant. Add 2 large eggs, 1 and 1/2 cups of whole milk, 1/2 teaspoon of lemon extract, and 1 teaspoon of lemon juice. Mix until smooth.
Melt 1 stick (4 ounces) of unsalted butter and let it cool slightly before adding it to the wet mixture.
Pour the wet ingredients into the bowl with the dry ingredients. Gently fold the mixture with a rubber spatula until just combined.
Fold in 1/3 cup of poppy seeds until evenly distributed throughout the batter.
Fill each muffin cup about two-thirds full with the batter.
Bake the muffins for 18-20 minutes, or until a toothpick inserted into the center comes out clean.
Allow the muffins to cool in the pan for about 5 minutes before transferring them to a wire rack. Prepare the glaze by whisking together 1 cup of confectioners' sugar, 2-3 tablespoons of lemon juice, 1 teaspoon of lemon zest, 1/4 teaspoon of salt, and optional 1/4 teaspoon of lemon extract. Drizzle the glaze over the cooled muffins.