Whisk all-purpose flour, whole wheat flour, flax seeds, hemp seeds, baking powder, cinnamon, and salt together in a bowl.
Whisk 1/2 cup warm milk, eggs, vegetable oil, and vanilla extract together in a separate bowl. Pour over flour mixture; mix until batter is just combined.
Combine 1/4 cup milk, brown sugar, cocoa powder, and butter in a small microwave-safe bowl. Heat in the microwave until butter is melted, 20 to 30 seconds. Stir well until sauce is smooth. Pour half of the sauce into another bowl; set aside.
Preheat a waffle iron according to manufacturer's instructions. Grease with cooking spray.
Spread a thin layer of batter in the iron using a spatula. Pour some of the chocolate sauce on top. Cover with another layer of batter. Close and cook until golden brown, 3 to 5 minutes. Repeat with remaining batter.
Drizzle reserved chocolate sauce over waffles before serving.