Preheat your oven to 375°F (190°C) and line a standard 12-cup muffin tin with paper liners or grease well with cooking spray. Measure all ingredients beforehand to streamline the mixing process.
In a medium bowl, whisk together the flour, baking soda, cinnamon, nutmeg, ginger, cloves, and salt. This thorough mixing ensures the spices and leavening agents distribute evenly throughout your muffins.
In a large bowl, whisk together the pumpkin puree, eggs, oil, granulated sugar, brown sugar, milk, and vanilla extract until smooth and well combined.
Add the dry ingredients to the wet ingredients and fold gently with a spatula just until combined. Stop when you no longer see dry flour streaks but can still see a few small lumps.
Fold in ¾ cup of the chopped pecans, reserving the remaining ¼ cup for topping. For enhanced nutty flavor, toast the pecans in a dry skillet over medium heat for 3-5 minutes until fragrant before adding them to the batter.
If using the crumb topping, combine the flour, both sugars, and cinnamon in a small bowl. Pour in the melted butter and mix with a fork until crumbly. Stir in the remaining chopped pecans.
Divide the batter evenly among the prepared muffin cups, filling each about ¾ full. If using, sprinkle the crumb topping generously over each muffin, pressing slightly to adhere.
Bake for 18-22 minutes, or until a toothpick inserted into the center comes out clean or with a few moist crumbs. Rotate the pan halfway through baking to ensure even browning.
Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.