Preheat the oven to 400 degrees. Line a muffin tin with wrappers. Spray with non-stick spray.
In a large bowl, combine flours, cocoa powder, baking powder, salt & sugar. Stir together until well combined.
In a second large bowl, crack the egg and whisk until it's frothy. Add the oil and whisk together. Add the vanilla and half of the milk. Pour the other half of the milk into the melted chocolate and stir together to cool. Pour the chocolate into the egg mix. Whisk together until well combined.
Pour the dry ingredients into the wet and fold together with a spatula, about 15 strokes. Fold in 1/4 C of the pistachios and 1/4 of the chocolate chips. Scoop into prepared muffin tin. Fill each muffin cup up to the top. Sprinkle the remaining nuts and chocolate evenly over the muffins. Place into preheated oven.
Bake for 2 minutes at 400 degrees, then lower the temperature to 375. Cook an additional 25-28 minutes until tops spring back when gently poked. Remove from oven to cooling rack.