Preheat oven to 375℉. Prepare a 12-cup muffin tin by either lining it with muffin cups, or lightly spraying it with nonstick spray.
Mash roasted butternut squash with a fork in a medium bowl, set aside.
In a large bowl, combine gluten-free all-purpose flour, almond flour, sugar, baking powder, cinnamon, nutmeg, and salt.
In another bowl, mix almond milk, maple syrup, coconut oil, ground flaxseeds, and vanilla.
Combine dry ingredients with wet ingredients and mix thoroughly. Fold in mashed butternut squash into the batter.
Spoon batter into prepared muffin cups. Sprinkle tops with extra sugar if desired.
Bake for about 30 minutes, or until a toothpick inserted in the middle of a muffin comes out clean. Allow the muffins to cool for about 10 minutes before removing from the pan. Enjoy!