Preheat and Prepare: Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or grease it thoroughly.
Combine Dry Ingredients: In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, ginger, nutmeg, and cloves. Set aside.
Mix Wet Ingredients: In a large bowl, whisk together the pumpkin puree, granulated sugar, brown sugar, and oil until well combined. Add the eggs and vanilla extract, and whisk until smooth.
Combine Wet and Dry: Gently fold the dry ingredients into the wet ingredients using a spatula, stirring until just combined. Be careful not to over-mix; a few lumps are okay.
Add Chocolate Chips: Toss the chocolate chips with a tablespoon of flour (this helps prevent sinking). Fold them into the muffin batter until evenly distributed.
Bake: Divide the batter evenly among the 12 muffin cups, filling them nearly to the top. Bake for 20-25 minutes, or until a toothpick inserted into the center of a muffin comes out clean or with just a few moist crumbs.
Cool: Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.