Preheat your oven to 375°F (190°C). Grease a muffin tin or line with paper liners.
In a large bowl, whisk together the flours, baking powder, baking soda, cinnamon, nutmeg, and salt.
In another bowl, mix the mashed sweet potatoes, brown sugar, vegetable oil, eggs, and vanilla extract until well combined.
Add the wet ingredients to the dry ingredients and stir until just combined. Do not overmix.
Gradually add the milk and stir until the batter is smooth.
Divide the batter evenly among the muffin cups.
Bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean.
Let the muffins cool in the tin for 5 minutes, then transfer to a wire rack to cool completely.