Heat 1 tablespoon of olive oil in a large pot or Dutch oven over medium-high heat. Add the eggplant and cook for 5-6 minutes, stirring occasionally, until lightly browned. Remove and set aside.
Add another tablespoon of oil to the pot. Add the zucchini and bell peppers and cook for 5 minutes until just starting to soften. Remove and set aside with the eggplant.
Add the remaining oil to the pot. Add the onion and cook for 4-5 minutes until softened, then stir in the garlic and cook for 1 minute until fragrant.
Stir in the crushed tomatoes and herbes de Provence. Bring to a simmer and cook for 5 minutes.
Return the eggplant, zucchini, and bell peppers to the pot. Season with salt and pepper, stir to combine, and simmer uncovered for 20-25 minutes, stirring occasionally, until all the vegetables are tender and the sauce has thickened.
Taste and adjust seasoning. Serve warm, garnished with fresh basil and thyme.