Riemannian manifolds with nonzero Killing spinors are Einstein manifolds. Kroncke proved that all complete Riemannian manifolds with imaginary Killing spinors are (linearly) strictly stable in [Stable and unstable Einstein warped products, preprint (2015), arXiv: 1507.01782v1]. In this paper, we obtain a new proof for this stability result by using a Bochner-type formula in [X. Dai, X. Wang and G. Wei, On the stability of Riemannian manifold with parallel spinors, Invent. Math. 161(1) (2005) 151-176; M. Wang, Preserving parallel spinors under metric deformations, Indiana Univ. Math. J. 40 (1991) 815-844]. Moreover, existence of real Killing spinors is closely related to the Sasaki-Einstein structure. A regular Sasaki-Einstein manifold is essentially the total space of a certain principal S-1-bundle over a Kahler-Einstein manifold. We prove that if the base space is a product of two Kahler-Einstein manifolds then the regular Sasaki-Einstein manifold is unstable. This provides us many new examples of unstable manifolds with real Killing spinors.