Preheat oven to 350 degrees. Grease a 12-count cupcake tray.
Squeeze the excess liquid out of carrots and zucchini. You want them to keep the cupcakes moist but not make them soggy.
Mix dry ingredients in a large bowl and set aside.
In another bowl, whisk eggs and apple sauce. Stir in grated zucchini , carrots and raisins (and optional flaxseed).
Add the wet ingredients to the dry ingredients and stir just until combined.
Fill cupcake trays until 3/4 full. Bake for approximately 20 minutes. They are done when a toothpick inserted comes out clean, and tops spring back when lightly touched.
Allow to cool in cupcake pan for 10 minutes before removing.
Store in an airtight container for up to 5 days.