Preheat oven to 350 degrees Fahrenheit and prepare a mini muffin tin with oil or liners. Set aside.
In a medium bowl, combine the flaxseed meal and water. Let it sit for 5-10 minutes, or until it has formed a gel.
Add in all the rest of the ingredients: applesauce, nut butter, oil, sugar, milk, vanilla, oat flour, almond flour, baking soda, baking powder, and salt. Mix until combined, then mix in the chocolate chips.
Scoop out the dough in 1 tablespoon-size scoops, or adjust based on the size of your muffin tin. Bake for 10 minutes.
Immediately after taking the cookies out of the oven, spray the back of a teaspoon with oil and press down into the center of each cookie to form the cup shape.
Return the tray to the oven and bake for an additional 5-10 minutes (for my oven it was 8) until the cookies are fully baked through. They are more fragile when hot, so let cool before removing from the pan.
Once cooled, fill the cups with whatever you desire. Some toppings I tried were strawberries, chocolate, peanut butter, yogurt, and cookie butter, but you can also try adding other fruits, granola, ice cream, or anything you can imagine!