Preheat the oven to 375°F and line every other muffin cavity with a liner.
In a large bowl, whisk together pumpkin puree, coconut sugar, vanilla extract, coconut oil, and almond butter until well combined.
In a separate bowl, mix all-purpose flour, baking soda, salt, cinnamon, and pumpkin pie spice.
Add dry ingredients to wet and mix with a spatula until just combined.
Use a double cookie scoop to fill muffin liners evenly and set aside.
In a medium bowl, beat softened cream cheese with sugar, milk, flour, and vanilla until light and fluffy.
Transfer cream cheese mixture to a piping bag or plastic baggie with a corner cut off. Pipe onto muffin tops.
Sprinkle pumpkin seeds or pepitas if desired, then bake for 23 minutes.
Let cool for 15-20 minutes before serving.