In this paper we present a stochastic scenariobased model predictive control (MPC) approach for the operation of islanded microgrids with high share of renewable energy sources. We require that the stored energy remains within given bounds with a certain probability using risk-based constraints as convex approximations of chance constraints. We show that risk constraints can generally be cast as conic constraints and, unlike chance constraints, can control both the number and average magnitude of constraint violations. Lastly, we demonstrate the risk-constrained stochastic MPC in a numerical case study.