Preheat oven to 350°. Line cookie sheets with parchment or silpat liners.
In large bowl, whisk together flour, cocoa, baking soda, and salt.
In a mixing bowl, cream together the butter, brown sugar, and sugar until light and fluffy. Add eggs one at a time. Add vanilla and mix until well blended.
Add the dry ingredients and mix until just blended. Stir in peanut butter chips and chocolate chips.
Using a small cookie scoop, drop by rounded spoonfuls on to cookie sheets. Bake 10 to 12 minutes, until edges are set but the center is still soft.
Allow cookies to cool on baking sheet for 5 minutes before removing to a wire rack to cool completely.