In this paper, we present a controller framework that synthesizes control policies for Jump Markov Linear Systems subject to stochastic mode switches and imperfect mode estimation. Our approach builds on safe and robust methods for Model Predictive Control (MPC), but in contrast to existing approaches that either optimize without regard to feasibility or utilize soft constraints that increase computational requirements, we employ a safe and robust control approach informed by the feasibility of the optimization problem. We formulate and encode finite horizon safety for multiple model systems in our MPC design using Control Barrier Functions (CBFs). When subject to inaccurate hybrid state estimation, our feasibility-guided MPC generates a control policy that is maximally robust to uncertainty in the system’s modes. We evaluate our approach on an orbital rendezvous problem and a six degree-of-freedom hexacopter under several scenarios and benchmarks to demonstrate the utility of the framework. Results indicate that the proposed technique of maximizing the robustness horizon, and the use of CBFs for safety awareness, improve the overall safety and performance of MPC for Jump Markov Linear Systems.