Preheat oven to 350 degrees F. Line 24 mini muffin cups, or 12 regular muffin cups, with paper liners.
In a large bowl, stir together flour, sugars, cinnamon, baking powder, baking soda and salt. In a smaller bowl, whisk eggs, oil, applesauce and vanilla. Add to flour mixture and stir until well combined. Fold in grated sweet potato and apple.
Spoon into lined muffin cups, filling 3/4 full. Bake for 13-15 minutes (for mini muffins) or 20-25 minutes (full-sized muffins), until golden and springy to the touch.