Preheat your oven: Set it to 350°F (175°C) and line a muffin tin with paper liners.
Mix the dry ingredients: In a bowl, whisk together the flour, baking soda, salt, cinnamon, and nutmeg.
Combine the wet ingredients: In another bowl, mix the pumpkin puree, sugar, eggs, and vegetable oil until fully combined.
Add the dry to the wet: Gradually add the dry ingredients to the wet mixture until just combined. Be careful not to overmix!
Prepare the cream cheese filling: In a small bowl, beat the cream cheese until smooth.
Fill the muffin cups: Spoon a portion of the batter into the muffin tins, filling each about halfway. Add a dollop of cream cheese on top, then cover with more batter until three-quarters full.
Bake: Place in the oven and bake for 20-25 minutes, or until a toothpick inserted comes out clean.
Cool down: Allow the muffins to cool in the pan for a few minutes before transferring them to a wire rack.