Preheat oven to 375 degrees F (190 degrees C). Spray a baking sheet with cooking spray.
Place 1 cup oats in a food processor; pulse 7 to 8 times. Add quinoa and pulse until finely chopped.
Transfer oat and quinoa mixture to a large bowl. Add remaining 1 cup oats, applesauce, eggs, sugar, vanilla extract, baking soda, and salt; mix well to combine. Fold chocolate chips and pecans into the batter.
Drop tablespoons of batter onto the baking sheet.
Bake in the preheated oven until edges are golden, about 14 minutes. Let sit on the baking sheet for 1 to 2 minutes before moving to a wire rack to cool, about 25 minutes.