Preheat oven to 350°F. Line a 12-cup muffin pan with paper liners.
Make the cinnamon crumb topping by combining ⅓ cup flour, ¼ cup brown sugar, and 1 teaspoon cinnamon. Cut in 3 tablespoons cold butter until mixture resembles coarse crumbs. Refrigerate.
Prepare cream cheese filling by beating 8 ounces softened cream cheese, ⅓ cup powdered sugar, and ½ teaspoon vanilla until smooth. Set aside at room temperature.
Make the pumpkin batter by whisking together 2 cups flour, baking powder, baking soda, salt, 2 teaspoons cinnamon, nutmeg, and cloves in a medium bowl.
In a large bowl, combine pumpkin puree, ¾ cup granulated sugar, ½ cup brown sugar, eggs, oil, and 1 teaspoon vanilla. Mix until smooth.
Fold dry ingredients into pumpkin mixture just until combined. Do not over-mix.
Assemble muffins by spooning 2 tablespoons batter into each cup. Add 1 tablespoon cream cheese filling in center. Top with more batter until cups are ¾ full.
Sprinkle crumb topping over each muffin, pressing gently to adhere.
Bake for 22-26 minutes until golden and toothpick inserted in pumpkin portion comes out with few crumbs. Cool 10 minutes in pan, then transfer to wire rack.