Preheat the oven to 350 degrees and grease a muffin tin with cooking spray.
First, make the cream cheese filling. In a small bowl, combine all the cream cheese filling ingredients. Mix until combined. Some clumps are ok, it likely won't be completely smooth! Set the bowl in the fridge to chill while you prepare the muffin batter.
To a medium bowl, add the dry ingredients: almond flour, coconut flour, cinnamon, pumpkin pie spice, baking soda and salt. Mix until combined and set aside.
In a large bowl, whisk together the wet ingredients: eggs, canned pumpkin, maple syrup, oil and vanilla. Whisk until smooth.
Add the dry ingredients into the wet ingredients. Mix gently until combined.
Using a spoon or a 1/4 measuring cup, scoop the batter evenly into the muffin tins.
Using a small spoon or a butter knife, create a small indent in the top of the batter to make room for the filling. Scoop a teaspoon or two of cream cheese filling into each indent.
Bake at 350 for 24 minutes. Let the muffins cool completely and then enjoy!