In a large bowl, combine the bocconcini, tomatoes, oil, salt, pepper flakes and some black pepper. Toss until fully combined.
Build the skewers: Thread basil, tomato, mozzarella and bread onto long wooden skewers; repeat in that sequence. Place the skewers on a baking sheet and drizzle oil over the bread. Set aside for 5 minutes to marinate, then drain off excess oil.
Grill, rotating constantly, until the cheese is warmed and the bread is toasted, 2 to 3 minutes. Serve immediately.