Heat the large Dutch oven over medium heat and add olive oil. Once shimmering, add the sliced onions and cook until they become soft and translucent, releasing a sweet aroma.
Add the minced garlic to the onions and cook for about 30 seconds, stirring constantly, until fragrant.
Stir in the sliced bell peppers and cook for 5-7 minutes, allowing them to soften and develop a slight char at the edges.
Add the diced eggplant and zucchini to the pot, stirring gently to combine all vegetables evenly. Cook for another 10 minutes, stirring occasionally, until the eggplant begins to brown.
Pour in the diced tomatoes with their juices, then sprinkle with dried thyme, salt, and pepper. Stir everything together to coat the vegetables evenly in the tomato sauce.
Reduce the heat to low, cover the pot with a tight-fitting lid, and let the vegetables braise slowly for about 60-90 minutes, stirring occasionally and checking that there’s enough liquid in the bottom. The vegetables should be tender and the flavors deeply melded.
Uncover the pot and gently stir the vegetables to assess their tenderness and flavor; adjust seasoning with salt and pepper as needed.
Once the vegetables are tender and the sauce has thickened to your liking, remove the pot from heat and serve the ratatouille hot, with crusty bread or over rice if desired.