Preheat the oven to 400 degrees F (200 degrees C). Line 9 muffin wells with cupcake liners or spray with nonstick spray.
Whisk powder drink mix, flour, baking soda, baking powder, and salt together in a medium bowl.
Whisk applesauce, yogurt, sugar, egg, and vanilla extract in a separate large bowl. Add the flour mixture; mix until just combined. Fold in chocolate chips.
Bake in the preheated oven for 7 minutes. Reduce heat to 350 degrees F (175 degrees C) and bake until muffins spring back when touched, an additional 10 to 12 minutes.
