In a medium bowl, combine flour, cocoa powder, baking soda, baking powder, and corn starch. Set aside.
In a large bowl, beat the apple butter, nut butter, sugars, and vanilla until smooth. Beat in dry ingredients until well combined, scraping down the sides of the bowl as necessary.
Fold in chocolate chips, and then refrigerate cookie dough for 30 minutes.
Preheat oven to 350 degrees F. Line two baking sheets with a silicone mat or parchment paper. Roll dough into 1-inch balls, then place on prepared baking sheets about 2-inch apart.
Bake for about 10 minutes until the edges are just set. Do not overbake!
Remove from oven and cool completely on cookie sheet. Store in an airtight container at room temperature for up to 1 week.