01 - Preheat oven to 400°F (200°C). Line a baking sheet with parchment paper. Toss bell pepper, zucchini, cherry tomatoes, and red onion with olive oil, salt, and black pepper until evenly coated.
02 - Spread prepared vegetables on the baking sheet and roast for 18 to 20 minutes, stirring halfway through, until tender and lightly caramelized. Remove from oven and allow to cool slightly.
03 - Reduce oven temperature to 350°F (175°C). Grease a 12-cup muffin tin or line with silicone liners.
04 - In a large mixing bowl, whisk eggs and milk until thoroughly combined. Gently stir in roasted vegetables, crumbled goat cheese, grated Parmesan, basil, thyme, and chili flakes if desired.
05 - Distribute the frittata mixture evenly into the muffin tin, filling each well about three-quarters full.
06 - Bake for 18 to 22 minutes or until the muffins are set and lightly golden on the surface.
07 - Let the frittata muffins cool in the tin for 5 minutes before carefully removing. Serve warm or at room temperature.