Bake in the preheated oven, stirring often, until toasted and fragrant, about 10 minutes. Remove from oven and cool, about 5 minutes.
Increase oven temperature to 400 degrees F (200 degrees C). Grease 12 muffin cups.
Mix millet, flour, cornmeal, poppy seeds, 3 tablespoons sugar, lemon rind, baking powder, baking soda, and salt together in a bowl.
Whisk milk, honey, canola oil, egg, and vanilla extract together in a separate bowl. Stir milk mixture into flour mixture until just combined. Pour batter into the prepared muffin cups; sprinkle 1 tablespoon sugar over batter.
Bake in the preheated oven until a toothpick inserted in the center of a muffin comes out clean and tops are golden, 12 to 15 minutes.