Preheat oven to 375 F. Grease an 8x8” pan or a small casserole dish with non-stick cooking spray.
In a large bowl, whisk together the eggs and almond milk. Add the diced onion, garlic, seasonings, parsley, basil, and melted coconut oil. Mix well. Stir in the coconut flour until no lumps remain.
Use a grater to slice the squash and carrots. Add to the bowl and mix until everything is combined.
Pour batter into greased baking dish and top with sliced tomatoes.
Bake (uncovered) for 50-60 minutes, or until browned. If top is starting to burn but the eggs are not set yet, cover the dish with aluminum foil and continue to bake until cooked through.