In this work, the stepped pressure equilibrium code (SPEC) (Hudson et al 2012 Phys. Plasmas 19 112502), which computes the equilibria of the multi-region relaxed magnetohydrodynamic energy principle (MRxMHD), has been upgraded to determine the MRxMHD stability in toroidal geometry. A theoretical formalism for SPEC is obtained by relating the second variation of the MRxMHD energy functional to the Hessian matrix, enabling the prediction of magnetohydrodynamic (MHD) linear instabilities. Negative eigenvalues of this matrix imply instability. Further, we demonstrate our method on simplified test scenarios in both tokamak and stellarator magnetic topologies, with a systematic comparison study between the marginal stability prediction of the SPEC with the ideal MHD stability code packages CAS3D and MISHKA-1.