Preheat your oven to 350° F and lightly oil and flour a 12-muffin baking sheet.
Whisk together the flours, starches, baking powder, baking soda, salt, cocoa powder, sugar, and dark chocolate chips.
Whisk together the apple cider vinegar and almond or soy milk until frothy. Add the vegetable oil and applesauce or pumpkin, then stir in the flax mixture. Add the wet ingredients to the dry and mix very well, until the batter is totally even and smooth (there's no gluten here to overdevelop, so don't worry about mixing too much). If the batter is stiff or very thick, add an extra 1-2 tablespoons non-dairy milk.
Scoop the batter into the muffin cups by the heaping 1/3 cup. Bake for 20 to 30 minutes, or until the muffins are firm on top. Cool completely before enjoying. The muffins will keep best when wrapped individually in plastic wrap and then stored in an airtight container.
Gena is a registered dietitian, recipe developer, and food blogger. She's the author of three cookbooks, including Power Plates (2017) and Food52 Vegan (2015). She enjoys cooking vegetables, making bread, and challenging herself with vegan baking projects.