01 - Preheat oven to 400°F. Line a baking sheet with parchment paper. Toss diced red bell pepper, zucchini, cherry tomatoes, and red onion with olive oil, salt, and black pepper. Spread evenly on the prepared baking sheet and roast for 18 to 20 minutes, stirring once halfway through, until vegetables are tender and slightly caramelized. Remove from oven and allow to cool slightly.
02 - Lower oven temperature to 350°F. Grease a 12-cup muffin tin or line the cups with silicone liners.
03 - In a large mixing bowl, whisk eggs and milk thoroughly until blended. Add roasted vegetables, crumbled goat cheese, grated Parmesan, chopped basil, dried thyme, and chili flakes if desired. Stir until evenly combined.
04 - Pour the mixture into the prepared muffin tin, filling each cup approximately three-quarters full.
05 - Bake for 18 to 22 minutes or until muffin tops are set and lightly golden brown. Remove from oven and let cool in the tin for 5 minutes before unmolding.
06 - Serve muffins warm or at room temperature according to preference.