We discuss the constraints that emerge from the existence of dimension-5 baryon-violating operators in the flipped SU(5) x U(1) superstring model. These are constraints on matter field assignments and on singlet VEV values. Although baryon-violating dimension-5 operators that appear as quintic non-renormalizable terms vanish as has been proven before and as we verify here, effective dimension-5 operators resulting from Higgs exchange put non-trivial but feasible constraints on the model. Constraints are also extracted from the presence of higher order non-renormalizable terms that generate such operators which do not a priori vanish.