Preheat the oven to 350°F (175°C). Line a muffin pan with paper liners.
Make the cream cheese filling: In a small bowl, beat together cream cheese, sugar, and vanilla until smooth. Set aside.
Prepare the muffin batter: In a medium bowl, whisk together flour, baking soda, baking powder, salt, cinnamon, nutmeg, and cloves.
In another bowl, whisk together pumpkin purée, sugar, oil, eggs, and vanilla until well combined.
Gradually stir the dry ingredients into the wet mixture until just combined. Do not overmix.
Fill muffin liners: Spoon a tablespoon of batter into each liner, add a small spoonful of cream cheese filling, and then top with more batter until liners are ¾ full. Swirl lightly with a toothpick.
Add topping: Mix nuts, brown sugar, and cinnamon, then sprinkle generously on top of each muffin.
Bake for 18–22 minutes, or until a toothpick inserted in the center comes out clean.
Cool slightly before serving warm.