Preheat oven to 400 degrees F (200 degrees C). Line 2 muffin tins with paper liners.
Mix oats, 1/3 cup sugar, lemon juice, wheat germ, water, and lemon zest together in a small bowl.
Mix cherries with 2 tablespoons sugar in a small bowl.
Combine remaining 2/3 cup sugar, flour, baking powder, cinnamon, and ginger in a large bowl. Stir in oat mixture. Mix in yogurt, eggs, oil, and butter until batter is thick and smooth.
Fold cherries into the batter. Divide batter evenly among muffin cups, filling each 3/4 full.
Bake in the preheated oven until tops start to brown and a toothpick inserted into the center comes out clean, 18 to 20 minutes. Cool in the tins for 5 minutes before transferring to a wire rack to cool.