Preheat your oven to 350°F (175°C) and line a standard 12-cup muffin tin with paper liners or grease thoroughly with cooking spray.
Prepare the zucchini by grating it on the large holes of a box grater. Using clean hands or a kitchen towel, squeeze out as much moisture as possible – this prevents soggy muffins.
Whisk together the dry ingredients in a medium bowl: flour, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves until well combined.
In a large bowl, beat together sugars and oil until smooth, about 1 minute. Add eggs one at a time, beating well after each addition.
Mix in the pumpkin puree, squeezed zucchini, and vanilla extract until just combined – the mixture might look slightly curdled, but that’s perfectly normal.
Gently fold the dry ingredients into the wet mixture using a rubber spatula, mixing just until no dry streaks remain. Overmixing will result in tough muffins.
If using nuts, fold them in now with just 2-3 strokes of your spatula.
Divide the batter evenly among the muffin cups, filling each about ¾ full. Sprinkle with pepitas if using.
Bake for 22-25 minutes or until a toothpick inserted in the center comes out clean or with just a few moist crumbs.
Cool in the pan for 5 minutes before transferring to a wire rack to cool completely.