Preheat oven to 375 degrees F. Spray a muffin tin with non-stick baking spray or line with paper liners.
In a large mixing bowl, add the flours, cocoa powder, instant coffee, baking powder, salt, and sugar. Whisk to combine.
In another large mixing bowl, add the egg, vanilla, almond milk, and melted coconut oil. Whisk until ingredients are combined.
Pour the wet ingredients into the dry ingredients and whisk until smooth. Scrape the sides and the bottom of the bowl with a spatula. Now, fold in the chocolate chips.
Using a measuring cup, pour the batter evenly into the muffin tin, about 2/3 of the way full each.
Bake the muffins in a preheated oven for 14-16 minutes. Insert a toothpick into the center, and if it comes out clean they are done.
Remove muffins from the oven and let cool for 10 minutes in the tin.
Remove the muffins from the tin and finish cooling on a wire rack or plate.