Preheat oven to 375 degrees F.
In a big bowl add the following ingredients and mix together with a spatula: flour, salt, baking powder, baking soda, cinnamon, nutmeg, and chia seeds.
In a second larger bowl add the wet ingredients and sugars: eggs, pumpkin puree, shredded carrots, shredded zucchini, applesauce, sugar, brown sugar. Mix well using a hand mixer (or a stand mixer).
Add about a quarter of the flour mixture to the wet mixture and carefully mix together with a spatula. Keep adding the flour mixture a quarter at a time until everything is well combined.
Spray your muffin tins with a non-stick cooking spray. You can make these into regular sized muffins or mini muffins. It should make about 24 regular muffins of 72 mini muffins.
Fill each cup 3/4 full, then bake for 22-25 minutes.
To test if they're done, put a toothpick in the center of a muffin and it should come out clean.