Preheat oven to 350 degrees Fahrenheit. Line a large cookie sheet with parchment paper.
Start with the chocolate cookie dough. In a medium bowl, whisk peanut butter, water, and maple syrup together until smooth. Add almond flour, cocoa powder, baking powder, baking soda, and salt. Stir to combine. Add vanilla extract and combine. Fold in chocolate chips.
Next, make your peanut butter dough. In a second medium bowl, whisk peanut butter, water, and maple syrup together until smooth. Add almond flour, baking powder, baking soda, and salt. Stir to combine. Add vanilla extract and combine. Fold in chocolate chips.
Cover and chill both doughs in the refrigerator for at least 30 minutes.
Using a tablespoon, scoop one tablespoon of the peanut butter cookie dough and roll together into a ball with your hands. (The dough will be sticky, so lightly wet your hands as needed to make rolling easier.) Scoop one tablespoon of the chocolate dough. Press it into the peanut butter dough ball and roll into one cohesive dough ball. Place ball on cookie sheet. Flatten about halfway down with palm of your hand. Continue until all dough is used up.(If either dough is too wet to roll into a ball, add a tablespoon of almond flour at a time.)
Bake for 12-13 minutes. Allow cookies to cool completely on cookie sheet. Store in an airtight container for 2-3 days. Cookies will soften over time.