Preheat oven to 350 F.
Combine flour, chia seeds, flaxseed, baking powder, cinnamon, and salt in a large bowl.
In a separate bowl, mix together applesauce, olive oil, honey, milk, and vanilla.
Pour wet ingredients into dry ingredients. Mix just until combined. Allow batter to sit for 5 minutes.
Spray muffin tin with nonstick baking spray. Pour 1/4 cup batter into muffin tin.
Bake for 15 to 18 minutes just until no longer doughy in the middle and slightly golden brown. Allow muffins to cool in muffin tin for about 5 to 10 minutes. Remove muffins and place on cooling rack.