Make the cream cheese filling: In a small bowl, mix the softened cream cheese, sweetener, and vanilla extract until smooth. Set aside.
Mix the dry ingredients: In a large bowl, mix the flour, pumpkin pie spice, baking powder, baking soda, and salt.
Mix the wet ingredients: In a separate bowl, whisk the eggs. Then add the pumpkin puree, brown sugar or sugar-free sweetener, applesauce, and vanilla extract. Whisk until combined.
Combine wet and dry: Pour the wet ingredients into the dry ingredients a little at a time, stirring until just combined. Don’t over-mix.
Prepare the muffin tin: Line a non-stick muffin tin with parchment paper liners or spray it with oil.
Fill the cups: Pour batter into each muffin cup, filling about ⅔ of the way full.
Add the cream cheese filling: Scoop slightly less than 1 tablespoon of the cream cheese mixture into the center of each muffin. A 1-tablespoon cookie scoop works great for this.
Bake: Bake the muffins at 350°F for 20-25 minutes, or until a toothpick inserted into the muffin (not the cream cheese center) comes out clean. Once done, let the muffins slightly cool, and enjoy!