Preheat oven to 425 degrees Fahrenheit and line a baking sheet with parchment paper. Set aside.
Pierce bratwurst multiple times each with a fork and add to a bowl with sliced onions and peppers. Set aside.
In a separate bowl, whisk together olive oil, vinegar, mustard, salt, red pepper flakes, and thyme. Pour over brats and vegetables and toss to coat.
Pour brats and vegetables onto prepared sheet pan and spread into a single layer. Bake for 30-35 minutes, flipping once halfway through, or until everything is browned and cooked through.
Stuff buns with bratwurst, top with onions and peppers, and serve immediately.
Leftovers will keep for 3-4 days in a sealed container in the refrigerator. Reheat in the microwave or in a 350 degree oven for 15 minutes, or until warmed through.
A half sheet pan will accommodate up to about 6 bratwurst with onions and peppers. If doubling recipe, divide ingredients between two half sheet pans and cook on two oven racks, rotating them halfway through. Spreading your ingredients out will help keep them from getting soggy as they roast.