Slice the eggplant, sprinkle each slice with a little sea salt on both sides, and then lay all the slices on dry paper towels to let the natural juices release, about 15 minutes.
Meanwhile, in a large pot, sauté the onions with 1 tablespoon olive oil on medium-high heat until golden, about 4 minutes. Add the mushrooms and garlic and sauté until the mushrooms are tender and the garlic is fragrant, about 2 minutes. Add in the heirloom tomato sauce, sugar or honey, oregano, thyme and pepper. Stir and bring to a simmer. Once simmering, turn off the heat and stir in the sweet peppers.
Preheat the oven to broil. Brush all the salt off of the eggplant slices and then with a pastry brush, brush each side of the eggplant slices with the remaining 2 tablespoons olive oil. Lay the eggplant slices in a single layer onto a rimmed baking sheet. Broil each side of the eggplant until golden brown, about 1-2 minutes on each side. Once the slices are golden, lay them on dry paper towels again. Once done with the eggplant, turn the oven down to 350 degrees F.
Now it’s time to assemble the eggplant parmesan casserole. In a 9 x 13 inch casserole dish, spoon in the sauce/mushroom/pepper mixture to cover a thin even layer on the bottom of the dish. Lay the eggplant slices on top of that in a single layer, then evenly sprinkle some of the basil and Parmesan cheese on top of that. Spoon over a little more of the sauce mixture, making sure to get the mushrooms and peppers evenly distributed. Cover that layer with slices of the mozzarella and more Parmesan. Repeat this process until all of the eggplant and sauce mixture is in the baking dish, ending with a layer of mozzarella slices and Parmesan.
Bake in the oven until the sauce starts to bubble on the sides, about 35 – 40 minutes. Remove from the oven and let sit for about 10 minutes. Sprinkle with fresh basil leaves, cut into squares and serve warm.
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