Preheat oven to 450°F; line a large sheet pan with parchment.
Whisk soy sauce, sesame oil, honey, garlic, ginger, and pepper flakes; reserve half in a separate clean bowl for beef.
Toss broccoli, peppers, and onion with sauce in first bowl. Spread in single layer on pan; roast 10 minutes.
Toss beef with reserved sauce. Remove pan; move vegetables aside and arrange beef in single layer.
Roast another 6 to 10 minutes, stirring once, until vegetables are tender and slightly charred and beef reaches desired doneness.
Serve immediately over rice or noodles, drizzled with pan juices.