Preheat your oven to 350°F (175°C) and grease a mini muffin tin or line with paper liners.
In a large bowl, whisk together the whole wheat flour, baking powder, baking soda, salt, cinnamon, nutmeg, and cloves.
In another bowl, mix together the pumpkin puree, brown sugar, vegetable oil, 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 prepared muffin cups, filling each about ¾ full.
Bake for 18-20 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
Allow the muffins to cool in the tin for a few minutes, then transfer to a wire rack to cool completely.