Preheat oven to 350°F. Lightly grease a baking sheet or line with parchment paper.
In a blender or food processor, add oats, cocoa, baking soda, baking powder, and salt. Blend until the mixture forms a fine flour. Set aside.
In a large bowl, add 3/4 cup Sunbutter and coconut sugar. Beat with an electric mixer until the ingredients are fully mixed, about 1 minute. Add applesauce, milk, and vanilla; stir to combine.
Slowly add the oat mixture to the large bowl while stirring, forming a soft dough. Keep folding the ingredients together until they are fully combined. Add chocolate chips; gently fold into the dough.
In a small bowl, add remaining 1/4 cup Sunbutter. Place the dough and Sunbutter in the fridge for up to 1 hour, at least 30 minutes. Stick the dough in the freezer to speed up the process.
Remove from the fridge. Form 10-12 balls of dough (about 1 1/2-inch in diameter). Flatten each ball 1/4-inch think; place 1 teaspoon Sunbutter in the center of the dough. Fold in the edges to ensure it isn’t oozing. Place the dough ball on the pan, seam side down. Flatten slightly. Repeat with all balls of dough.
Bake for 13-15 minutes, until the edges of the cookies are slightly crispy. Remove and let cool for 10 minutes before serving.