Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners or grease it lightly.
In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and nutmeg.
In another bowl, mix the butternut squash puree, vegetable oil, sugar, eggs, and vanilla extract until well combined.
Gradually add the wet ingredients to the dry ingredients, stirring until just combined. Do not overmix.
Divide the batter evenly among the muffin cups, filling each about ⅔ full.
Bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.