Heat oven to 375 degrees F. Grease 12-cup muffin tin.
Combine flour, sugar, poppy seeds, baking powder, baking soda, and salt together in a large bowl.
In a separate bowl, mix yogurt, lemon zest, and eggs until smooth.
Gently fold yogurt mixture into flour mixture and stir until just combined.
Fold in melted butter; Do not overmix.
Divide batter evenly among prepared muffin cups.
Bake 20 to 25 minutes. Rotate muffin tin halfway through baking.
While muffin are baking, simmer sugar and lemon juice together in a small saucepan over medium heat until it turns into a light syrup, about 3-5 minutes.
Remove muffin tin to a wire rack.
Brush with lemon syrup.
Let muffins cool in tin for 5 minutes, then transfer to a wire rack and let cool for another 10 minutes before serving.