Preheat the oven to 400 degrees. Season the cooked spaghetti squash with salt and pepper. If you have made it ahead of time and stored it in the fridge, make sure to bring it to room temperature before cooking.
Grease a pie plate with coconut oil, then press the spaghetti squash into the plate and up the sides to form a crust.
Slice the tomatoes into thin slices and drain on paper towels.
Saute the zucchini, bell pepper, and red onion in olive oil until tender. Remove from heat and set aside.
Meanwhile, whisk together the eggs, coconut milk, salt, dry mustard, pepper, garlic powder, and half of the basil. Whisk in one spoonful of the cooked veggie mixture at a time to avoid scrambling the eggs by adding all the hot veggies at once.
Place half of the sliced tomatoes in the bottom of the crust. Pour in the egg and veggie mixture, then arrange the remaining tomato slices on top.
Bake the quiche until the center is set when the plate is tapped and the spaghetti squash crust gets crispy (around 30-45 minutes).