Heat olive oil in a large skillet or Dutch oven over medium heat.
Add the onions and garlic, and sauté until the onions are translucent and the garlic is fragrant, about 2-3 minutes.
Add the bell pepper, eggplant, and zucchini to the skillet. Cook for about 5-7 minutes, stirring occasionally, until the vegetables start to soften.
Stir in the chopped tomatoes, salt, black pepper, and red pepper flakes (if using). Bring to a simmer.
Reduce the heat to low and cover the skillet. Let it simmer for 20-30 minutes, stirring occasionally, until all the vegetables are tender and the flavors have melded together.
Stir in the fresh basil and thyme. Adjust seasoning with additional salt and pepper if needed.
Enjoy your meal!