Gather all ingredients. Preheat the oven to 400 degrees F (205 degrees C). Lightly grease a 12-cup muffin pan.

Combine flour, 3/4 cup sugar, poppy seeds, baking powder, baking soda, and salt in a bowl.

Mix eggs, yogurt, oil, and lemon zest together in a separate bowl until well blended. Pour over flour mixture, then mix until just combined.

Spoon batter evenly between the prepared muffin cups, filling each 3/4 full.

Bake in the preheated oven until tops spring back when lightly pressed, about 15 minutes. Let muffins cool in the pan for 5 minutes.

Meanwhile, make the glaze: Stir lemon juice and 3 tablespoons sugar together until sugar dissolves.

Pierce the top of each muffin several times with a wooden skewer while they are still warm. Slowly pour about 1 tablespoon lemon glaze over the top of each muffin.

Let muffins continue to cool in the pan until glaze has set, about 10 minutes more.