Preheat oven to 325° F. Line large, rimmed baking sheet with parchment paper. Place popcorn in large mixing bowl.
In small saucepan over medium heat, combine sugar, butter, honey and salt; bring to light boil, stirring often, until melted.
Pour sugar mixture over popcorn. Add coconut flakes and chia seeds; toss gently to combine.
Spread mixture on prepared baking sheet. Bake about 30 minutes, or until popcorn is lightly toasted. Let cool completely; break into clusters for serving.