Preheat the oven to 400 degrees F.
Poke holes in the butternut squash with a fork.
Place the butternut squash in the microwave and cook until it is tender, about 10-15 minutes, checking every 3 minutes. Let cool for about 15 minutes.
Once cooled enough to touch, cut the butternut squash in half, scoop out the seeds and discard, and then scoop out the flesh, placing it in a bowl. Mash it with a fork.
Measure 1 ½ cups of the butternut squash puree.
Grease 18 muffin cups
In a large bowl, add the 1 ½ cups butternut squash puree, eggs, oil, milk, granulated sugar, and brown sugar, and mix well.
Add the baking powder, baking soda, cinnamon, salt, nutmeg, and cloves and fold into the batter until just combined.
Fold in the flour.
Fold in the pecans, if using.
Spoon the batter into the prepared muffin pans, about ⅔ full.
Bake in the preheated oven 13-16 minutes, until a toothpick comes out clean.
Cool in the pans for about 5 minutes and then remove the muffins and cool completely on a wire cooling rack.
Serve topped with butter, nut butter, or plain! Enjoy!