In a large mixing bowl, whisk together all of the wet ingredients until smooth and well combined.

Add the freshly milled flour, cocoa powder, and salt to the bowl with the wet ingredients. Gently stir just until incorporated. Cover and set aside to let the flour absorb the liquid for 10 minutes.

After resting, sprinkle in the baking powder and baking soda. Mix gently until everything is evenly combined, being careful not to overmix. Fold in the chocolate chips.

Working quickly, spoon the batter into the prepared muffin tin, filling each cup evenly.

Optional: For a pretty (and delicious) peanut butter swirl top, spoon a small dollop of creamy peanut butter on top of each muffin. Using a knife or toothpick, swirl the peanut butter into the chocolate batter. Additionally, press a few chocolate chips to the top of each muffin.

Bake at 425°F for 5 minutes, then reduce the oven temperature to 350°F (175°C) and continue baking for 10-12 minutes, or until the centers feel firm and the muffins are baked through. Be careful not to overbake muffins with cocoa powder, as they dry up very quickly.

Remove from the oven and let cool slightly on a wire rack — or enjoy warm right away.

Store cooled muffins in an airtight container at room temperature for up to 2 days. For longer storage, freeze the muffins the same day they’re baked. Thaw at room temperature before serving.