Preheat the oven to 350°F (177°C) and bring the ground beef to room temperature.
Cut the tomatoes in half to create two 'half-cups'. Scoop out the inside of the tomatoes with a spoon. Sprinkle the insides of the tomatoes with a pinch of salt and lay upside down on a plate to drain.
Cut the bell peppers in half and remove the seeds. Cut the zucchini in half lengthwise and scoop out the flesh with a small pointed spoon, to create little boats.
Peel the onion and cut it in half, then separate the individual layers so they are like cups. If the bottom of any of the onion cups has a hole, cut a slice of onion layer to patch it.
Grease 2 large ovenproof dishes with butter and place all the veggable cups in them.
In a large bowl, add the ground beef, garlic, egg, coconut flour, 1 teaspoon of salt, pepper and nutmeg. Mix well, with your hands or a spoon, until well blended. Pour the melted butter over the mix and stir to incorporate. The mix should be soft but not runny.
Fill the veggable cups with meat mixture, distributing it evenly.
Bake for 45 minutes to 1 hour, depending on the size of the veggables and desired doneness.
Serve immediately, with a salad. This dish can be also eaten cold.