In a large mixing bowl, whisk together the granulated sugar, brown sugar, 1 1/2 cups flour, baking soda, baking powder, salt, and poppy seeds.
Mix in the eggs, milk, oil, and almond extract until the batter forms. Do not overmix. Transfer the batter to the fridge to chill while preheating the oven to 350F.
Prepare a muffin pan with paper liners. Once the oven has preheated, toss the chopped cherries in the remaining flour and gently fold them into the batter. Fill each muffin pan well halfway full with batter.
Bake the muffins for 28 minutes until the tops are fully set and lightly golden brown. Let cool.
To glaze, whisk together the powdered sugar, milk, and almond extract. Drizzle the glaze over the tops of the muffins.