Preheat the oven to 350° F. Lightly coat 16 muffin cups (preferably silicone) with cooking spray. Heat oil over medium in a large skillet. Add onion and cook until clear, about 8 minutes. Add cauliflower and cook about 4 minutes, until soft. Season with salt. Add quinoa and cook stirring frequently to heat through and incorporate.

In a large bowl, whisk eggs and stir in the cheddar cheese, quinoa mixture, and tomatoes, until well combined. Use a ¼-cup measuring cup to divide the mixture evenly into the prepared muffin cups. Sprinkle tops of each with ⅛ teaspoon parmesan cheese. Bake until the eggs are set, 18-20 minutes. Cool completely before transferring from molds to a freezer bag before freezing.