Preheat the oven to 375°F. Lightly grease 2 baking sheets.
In a medium bowl, whisk together the flour, baking soda, and salt, then set aside.
Blend the applesauce, brown sugar, and vanilla extract with an electric mixer until smooth. Add the egg and mix well.
¼ of a cup at a time, add the flour mixture to the applesauce mixture, blending well after each addition.
Fold in the muesli and dark chocolate chips.
Scoop a tablespoon of the dough at a time and drop it onto the prepared baking sheet. You should get about 15 cookies per pan.
Place in the oven and bake for 6 minutes.
Rotate the pans top-to-bottom and front-to-back, then bake for another 5 to 6 minutes.
Remove the cookies from the oven and let them cool on the pans for 5 minutes.
Transfer the cookies to a wire rack to cool completely.