Preheat and prep: Heat the oven to 375°F (190°C).
Line a 12-cup muffin tin with paper liners or grease lightly.
Mix dry ingredients: In a large bowl, whisk the whole wheat pastry flour, all-purpose flour, baking powder, baking soda, and salt. If using poppy seeds, add them now.
Combine wet ingredients: In a medium bowl, whisk the eggs, Greek yogurt, oil, honey, lemon juice, lemon zest, vanilla, and milk until smooth.
Bring it together: Pour the wet mixture into the dry ingredients. Stir gently with a spatula until just combined.
A few small lumps are fine. Do not overmix.
Fill the pan: Divide the batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle with a little coarse sugar if you like a crisp top.
Bake: Bake for 15–18 minutes, or until the tops are set and a toothpick comes out with a few moist crumbs.
Cool: Let the muffins cool in the pan for 5 minutes, then move them to a wire rack. If glazing, cool completely first, then drizzle with the lemon glaze.
Serve: Enjoy warm or at room temperature.
The lemon flavor develops even more by the next day.