Preheat oven to 375 degrees F (190 degrees C). Line muffin cups with aluminum foil liners.
Mix almond butter, banana, cocoa powder, ground flax seeds, honey, vanilla extract, and baking soda together in a bowl until batter is well blended; fold in zucchini and semisweet chocolate chips. Scoop batter into the prepared muffin cups. Top each with bittersweet chocolate chips.
Bake in the preheated oven until a toothpick inserted into the center comes out clean, about 25 minutes. Place muffins on a wire rack to cool.