Preheat and prep: Heat your oven to 375°F (190°C). Line a 12-cup muffin pan with paper liners or lightly grease it.
Mix dry ingredients: In a medium bowl, whisk flour, baking powder, baking soda, salt, cinnamon, nutmeg, ginger, and cloves until combined.
Whisk wet ingredients: In a large bowl, whisk eggs and sugar until smooth and slightly lighter.
Add oil, pumpkin puree, milk, and vanilla. Whisk until fully blended.
Combine gently: Add the dry mixture to the wet ingredients. Stir with a spatula until just combined. Do not overmix; a few small lumps are fine.
Fold in extras: If using chocolate chips, nuts, or cranberries, fold them in now.
Save a few for the tops if you like.
Fill the pan: Divide the batter evenly among the muffin cups, filling each about 3/4 full. Sprinkle with pepitas or coarse sugar if using.
Bake: Bake for 18–22 minutes, or until a toothpick comes out clean or with a few moist crumbs. Tops should spring back when lightly pressed.
Cool: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack.
Cool at least 10 more minutes before serving.