Heat olive oil in a large skillet over medium heat until shimmering, then add the eggplant cubes. Cook, stirring occasionally, until they soften and turn golden brown, about 8-10 minutes.
Add sliced zucchini to the skillet along with a pinch of salt. Cook together, stirring gently, until zucchini begins to soften, about 5 minutes.
Stir in chopped bell peppers and minced garlic, cooking for another 3-4 minutes until fragrant and peppers start to soften.
Add diced tomatoes and fresh thyme, stirring well. Reduce heat to low, cover partially, and let simmer gently for about 20-25 minutes, stirring occasionally, until the vegetables are tender and the flavors meld.
Taste and season with salt and freshly ground pepper as needed, then cook for another 5 minutes uncovered to thicken the sauce slightly.
Remove from heat and serve the ratatouille hot, garnished with extra thyme if desired, and enjoying the colorful, fragrant vegetable stew.