Preheat the oven to 400°F. Lightly grease a large baking dish. Make three diagonal cuts on each side of the fish through the thickest part of the flesh to ensure even cooking.

Combine the garlic, harissa, and olive oil in a small dish. Put 2 teaspoons of the harissa mixture in the fish cavity and spread the remainder over both sides of the fish, rubbing it into the slits. Place two lemon slices in the cavity of the fish.

Arrange the onion slices in a layer on the baking dish. Top with the tomato slices, thyme, and remaining lemon slices. Place the fish on top and bake, uncovered, for about 25–30 minutes, or until the flesh is opaque. Transfer the onion and tomato to a serving dish. Place the fish on top and season with salt.