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Preheat the oven to 350 degrees F. Coat a muffin tin with nonstick spray or line with paper liners.
In a small bowl, melt the butter. Set aside to cool to room temperature.
In large bowl, whisk together the whole wheat flour, all-purpose flour, baking powder, baking soda, salt, and poppy seeds. Set aside.
Place the sugar in a medium bowl and add the lemon zest. With your fingers, rub the two together until the sugar is moist and fragrant.
Add the yogurt, eggs, lemon juice, vanilla, and melted butter. Whisk until smooth.
Make a well in the center of the dry ingredients, then carefully pour in the wet ingredients. Mix gently just until the flour disappears.
With a scoop, divide the batter evenly between the muffin cups (they'll be ⅔ to ¾ of the way full).
Bake for 18 to 20 minutes, or until a toothpick inserted in the center comes out clean.
Let cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.
While the muffins cool, make the glaze: whisk together the lemon juice and powdered sugar until smooth. Drizzle over the cooled muffins.