Preheat your oven to 375°F (190°C). Line a muffin tin with paper liners.
In a medium bowl, whisk together the flour, baking soda, salt, cinnamon, nutmeg, and cloves.
In a large bowl, mix together the pumpkin puree, vegetable oil, eggs, and sugar until well combined.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
In a separate bowl, beat the cream cheese, sugar, and vanilla extract until smooth.
Fill each muffin cup with a small amount of batter, then add a spoonful of the cream cheese mixture. Top with more batter until each cup is about ¾ full.
Bake for 18-20 minutes, or until a toothpick inserted into the muffin part comes out clean. Let cool before serving.