Preheat oven to 425 degrees F (220 degrees C). Spray 24 mini-muffin cups with cooking spray.
Heat a skillet over medium-high heat. Cook and stir beef and onions in the hot skillet until browned and crumbly, 5 to 7 minutes. Drain excess fat and set aside to cool.
Combine flour, white sugar, baking powder, and salt in a large bowl. Whisk milk, ketchup, melted butter, eggs, and mustard together in a separate bowl; stir into flour mixture until just moistened. Fold ground beef mixture and Cheddar cheese into batter; spoon into each muffin cup.
Bake muffins in preheated oven until a toothpick inserted into the center comes out clean, about 15 minutes.