Preheat an oven to 180c (350f) and prep a 12-cup muffin pan with paper liners.
Into a large mixing bowl, add the pumpkin puree, oil, eggs, cinnamon, nutmeg, pumpkin pie spice, milk, sugar, brown sugar, vanilla extract, and salt, and mix with a whisk until well combined.
Add the flour, baking soda, and baking powder, and mix with a whisk until just combined and there are no lumps of flour visible. Set aside while you make the cream cheese filling.
In a small mixing bowl, add the cream cheese, sugar, and vanilla extract and mix until well combined and creamy. Transfer the cream cheese mixture into a piping bag and cut off the tip.
Pour the batter into the muffin tins filling almost to the top using an ice cream scooper or a large cookie scooper. Pipe about 1 teaspoon of the cream cheese filling on top of each muffin.
Top each muffin with the cinnamon sugar.
Bake in a 200c (400f) preheated oven for 5 minutes, and then bake for another 10-12 minutes at 180c (350f) or until a toothpick comes out clean with a few moist crumbs.
Notes
Use pure pumpkin puree in this recipe! It is very important that you use pure pumpkin puree in this recipe. Make sure that you are not using the presweetened or pre-spiced pumpkin puree. You will be able to find this information on the ingredient list of your pumpkin puree can.
Use room temperature ingredients. It is important that you use room-temperature ingredients. This step ensures that your mixture mixes into a homogenous mixture and bakes perfectly. you don’t want to place cold batter into the oven.
Let your cream cheese come to room temperature before mixing. This helps it blend smoothly without lumps.
Even distribution. Make sure each muffin has an equal amount of batter and filling to ensure consistent baking.
Don’t overmix the batter, you don’t want to develop the gluten in the flour. This step ensures you have moist muffins and not dense and dry muffins.
Measure your flour correctly! When measuring your flour, avoid scooping it with a measuring cup. Instead, stir the flour with a spoon to create as many air pockets as possible, and spoon it into your measuring cup. Finally, level it with a back of a knife.
Avoid overbaking! Check your muffins a few minutes before the recommended baking time. They're done when a toothpick inserted in the center comes out clean or with just a few moist crumbs.
Use an ice cream scoop or large spoon to fill each muffin cup about ⅔ full. This allows room for the muffins to rise without overflowing.
Cool before serving. Allow muffins to cool in their pan for about 10 minutes before transferring them to a wire rack to cool completely, which helps set the filling inside.