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This paper proposes embedded Gaussian Process Barrier States (GP-BaS), a methodology to safely control unmodeled dynamics of nonlinear system using Bayesian learning. Gaussian Processes (GPs) are used to model the dynamics of the safety-critical system, which is subsequently used in the GP-BaS model. We derive the barrier state dynamics utilizing the GP posterior, which is used to construct a safety embedded Gaussian process dynamical model (GPDM). We show that the safety-critical system can be controlled to remain inside the safe region as long as we can design a controller that renders the BaS-GPDM's trajectories bounded (or asymptotically stable). The proposed approach overcomes various limitations in early attempts at combining GPs with barrier functions due to the abstention of restrictive assumptions such as linearity of the system with respect to control, relative degree of the constraints and number or nature of constraints. This work is implemented on various examples for trajectory optimization and control including optimal stabilization of unstable linear system and safe trajectory optimization of a Dubins vehicle navigating through an obstacle course and on a quadrotor in an obstacle avoidance task using GP differentiable dynamic programming (GP-DDP). The proposed framework is capable of maintaining safe optimization and control of unmodeled dynamics and is purely data driven.