01 - Preheat oven to 400°F and line a baking sheet with parchment paper.
02 - Combine 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 halfway through, until vegetables are tender and caramelized. Remove from oven and allow to cool slightly.
03 - Reduce oven temperature to 350°F. Grease a 12-cup muffin tin or use silicone muffin liners.
04 - In a large mixing bowl, whisk eggs with milk until fully incorporated. Fold in roasted vegetables, crumbled goat cheese, Parmesan, basil, thyme, and chili flakes if using.
05 - Evenly divide the egg mixture among the muffin cups, filling each about three-quarters full.
06 - Bake at 350°F for 18 to 22 minutes until muffins are set and lightly golden on top.
07 - Allow muffins to cool in the tin for 5 minutes before removing. Serve warm or at room temperature.