In a medium mixing bowl, whisk together the all purpose flour, rye flour, cocoa powder, baking powder, baking soda, and salt.
In a large mixing bowl, whisk together the melted butter, sugar, brown sugar, sourdough starter, eggs and vanlla extract.
Add the flour mixture to the sourdough starter mixture and stir until well combined.
Stir in the chocolate chips. The dough will be very soft.
Cover and chill the dough for at least 2 hours. You can also chill it up to three days. The more time you give the dough in the fridge, the more distinct the sourdough taste will be.
Preheat the oven to 350 F.
Line a baking sheet with parchment paper or a silicone baking mat.
Using a 2 tablespoon cookie scoop, place balls of dough onto the prepared baking sheet about 2 inches apart.
Use a flat bottomed glass to gently press and flatten the dough into a disc.
Sprinkle with flaky sea salt.
Bake the cookies on the middle rack of the oven until set and slightly puffy, about 8-12 minutes.
Allow the cookies to cool on the baking sheet for 5 minutes before transferring to a wire rack.
Repeat for remaining cookies.
Notes
These cookies store best in an airtight container on the counter for 3-4 days!These cookies also freeze really well! Once they are totally cooled, place them in a sealed freezer bag or container and freeze for up to 2 months. Make sure to label them so you don’t forget what they are!