Preheat the oven to 350 degrees F and remove the middle rack from the oven. Grease a bundt cake with non-stick cooking spray and set aside.
Filling: use an electric mixer to combine all ingredients, and mix until smooth and creamy. Set aside for now.
Cake: in a large bowl, use an electric mixer to combine the applesauce, Greek yogurt, sugar, eggs, almond milk, and vanilla.
Add the flour, cocoa powder, instant coffee, baking powder, and baking soda. Mix until well-incorporated.
Add the boiling water and mix well. If using chocolate chips, fold those in here.
Pour about 1/3 of the batter into the greased bundt pan and spread it around evenly. Pour all of the cream cheese filling on top, and spread it around evenly.
Add the remaining cake batter on top of the cheesecake layer, and then place the pan in the oven.
Bake for 60-70 minutes, or until the center is set and a toothpick inserted into the center comes out clean.
Remove from oven and allow to cool for at least 30 minutes. Place a plate on top of the pan and flip the pan upside down to remove cake from pan. If cake does not come out, lightly tap the pan, or use a knife to loosen the edges.
Allow the cake to completely cool before frosting. To make the frosting, combine all of the ingredients with an electric mixer. If mixture is too thick, add extra liquid, and likewise, if frosting is too thin, add a bit more powdered sugar.
Slice the cake and enjoy!