Preheat oven to 350°F. Spray a mini muffin tin with nonstick spray or coat with coconut oil. Set aside.
Make flax eggs by combining water and flax seeds in a small bowl. Stir to combine then set aside.
In a medium bowl, whisk together almond butter, light brown sugar, maple syrup, unsweetened applesauce and melted coconut oil. Whisk until combined.
Add cocoa powder in ¼ cup increments, whisking until shiny and smooth. Scrape down the sides of the bowl as necessary. Whisk in vanilla, salt and flax eggs, mixing until well incorporated. Using a rubber spatula, fold in almond flour and baking powder until you get the consistency of soft dough or very thick batter, and no flour patches remain.
Combine your dairy free cream cheese and granulated sugar and mix well.
Using a 1-tablespoon cookie scoop and drop a little over 1-tablespoon of batter into each muffin cup. Shake the pan repeatedly, until batter is even. Next, add a 1/2 teaspoon of the cream cheese mixture on top of each brownie muffin.
Bake for 20 minutes. Immediately top each brownie with 2-3 chocolate chips. Cool in pan for 25 - 30 minutes until completely cool.
Using a knife, gently go around the edges of each brownie bite and release from the pan. Cool completely on wire rack.
Store for up to 3 days in the refrigerator. May also be stored in freezer safe container.