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Heat grill or grill pan to medium-high. Spread eggplant slices on a sheet of paper towels and sprinkle with 1/4 teaspoon salt. Set aside to drain. Blot with paper towels.
In a small bowl, blend the remaining 1/4 teaspoon salt, vinegar and mustard. While whisking, add oil in a thin stream. Whisk in pepper.
Brush eggplant and onion with some of the dressing and grill 4 minutes per side, turning once. Remove to a platter. Brush zucchini with dressing and grill 3 minutes per side, turning once (this may need to be done in batches). Transfer to platter. Refrigerate overnight.
Heat oven to 350°F. Slice bread lengthwise in half. Spread each cut side with 1/4 cup pesto. Divide eggplant slices between loaves. Top with zucchini, onion, cheese and roasted peppers. Replace top crusts and wrap loaves in foil.
Bake for 20 minutes, weighing down with a cast-iron skillet or foil-wrapped brick. Unwrap loaves and bake an additional 10 to 15 minutes, until cheese is melted and sandwiches are warm throughout. Cut each loaf into 8 slices.