Preheat oven to 180C/350F. Spray a casserole dish with non-stick spray and set aside.
In a large bowl, whisk the eggs and milk together until thoroughly combined. Add the ham and spinach and mix gently to combine. Add salt and pepper to season.
Arrange the veggies into the prepared pan. Pour the egg mixture on top and sprinkle with nutritional yeast.
Bake for 35-45 minutes or until filling is set and no longer jiggles. Cool for 10 minutes on a wire rack before slicing and serving.
Store tightly covered in a refrigerator for up to 4 days.