Preheat your oven to 375°F (190°C) and grease a muffin tin or line with paper liners.
In a large mixing bowl, whisk together the butternut squash puree, sugar, almond milk, and vegetable oil until well combined.
In another bowl, sift together the flour, baking powder, baking soda, cinnamon, nutmeg, and salt.
Gradually add the dry ingredients to the wet 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.
Allow the muffins to cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.