Preheat oven to 375°. Heat olive oil in a large, heavy ovenproof frying pan (not nonstick) over high heat until oil is hot but not smoking. Add chicken breasts, top side down, and cook until golden, 2 to 3 minutes. Turn chicken over.
Add shallots and garlic to pan with chicken, stirring occasionally so garlic doesn't burn, until shallots are soft and translucent, 3 to 4 minutes. Add chicken stock, roasted red peppers, cannellini beans, 1/2 tsp. salt, 1/4 tsp. pepper, and red pepper flakes and cook until mixture begins to boil, about 1 minute.
Cover pan and put in oven. Bake 14 to 16 minutes, or until chicken is just cooked through (cut to check). Transfer chicken to a plate.
Season roasted red pepper-cannelini bean-stock mixture with salt and pepper to taste and stir in lemon juice and zest. Divide vegetables among 4 rimmed plates or shallow pasta bowls, top each with a piece of chicken, and spoon sauce over all. Garnish with parmesan.