Preheat oven to 450. Line a baking sheet with a rack.
Remove stem and cut eggplant into six 1/4 inch thick slices. Lay slices on prepared rack, brush with 2 tbsp oil, and season with salt and black pepper. Roast eggplant in oven, 8 minutes per side; remove and cover with foil.
Combine goat cheese, ricotta, lemon juice and zest, thyme, pepper flakes, and salt for filling.
Heat 2 tbsp oil in a saucepan over medium heat. Add onion and garlic; cook 1 minute. Stir in tomatoes, bell pepper, wine and tomato paste; cover, reduce heat, and simmer 10-12 minutes, stirring often. Puree mixture in a food processor with basil and half-and-half; season with salt and pepper.
Spoon 1/4 cup sauce into two small casserole dishes. Spread 1 tbsp filling on each eggplant slice, roll, then place three rolls, seam down, in each dish. Top rolls with more sauce, mozzarella, and almonds. Bake rolls until golden, 15-20 minutes.
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