Preheat oven to 400 degrees F. Grease 12 muffin cups or line with paper liners.
2
Combine flours, sugar and 1/2 chips, cocoa powder, and baking soda in a large bowl. Set aside.
3
Whisk flaxseed paste, yogurt, milk, and pumpkin in another bowl until smooth (add extra milk by tbsp if too think); pour into chocolate mixture and stir until batter is just blended. Fill prepared muffin cups 3/4 full and sprinkle with remaining 1/4 cups chocolate chips.
4
Baked in preheated oven until toothpick inserted into the center comes out clean, about 20 minutes. Cool in the pan for 10 minutes before removing to cool completely on a wire rack.
