Preheat the oven to 350 degrees Fahrenheit. Grease a 9x5 loaf pan with coconut oil or cooking spray and then line with parchment paper. Allow parchment to hang over each side slightly.
Prepare your flax eggs in a small bowl and set aside. Place ⅔ cup chocolate chips in a small microwave-safe bowl. Heat for 30 seconds, then stir until remaining chips are melted. Set aside to cool.
Add the almond flour, cocoa powder, salt, baking soda, and baking powder in a medium bowl. Whisk to combine.
Combine the applesauce and maple syrup in a separate bowl. Whisk until incorporated. Add flax eggs, almond butter, and vanilla extract, whisk to combine. Fold in cooled melted chocolate.
Add the dry ingredients to the wet ingredients and stir until thoroughly integrated (the batter will be thick). Pour the batter into prepared pan and smooth top with a spatula.
Bake for 55-60 minutes or until a tester comes out mostly clean. Allow cake to cool completely in pan on a wire rack. (This is a dense, moist cake, it may sink slightly in the middle.)
Once loaf cake has cooled, prepare the chocolate ganache: Combine the chocolate chips and almond milk in a small microwave-safe bowl. Heat for 30 seconds, then stir until remaining chocolate chips are melted.
Remove cake from pan using the parchment 'handles' and transfer to a cutting board or serving plate. Pour chocolate ganache over top of cake and smooth with a back of a spoon. Ganache will harden as it cools. Slice with a sharp knife and serve. For a cleaner slice, wipe knife with a damp paper towel after each cut.
Cake is best the day it is made but can be stored in an airtight container for 2-3 days.