Spin state (SS) transitions in metal-containing pyramidal complexes that originate from crystallographic distortions are the research subject of this work. The transition elements are considered to be in the 3d 6 configuration (Fe 2+, Co 3+), and they display three different SSs: low-spin (LS, S= 0), intermediate-spin (IS, S= 1) and high-spin (HS, S= 2) states. They have been studied in the frame of the crystal field approximation via the effective nuclear charge Z eff and under oxygen cage distortions. The features of the SS stability have been calculated with/without accounting for spin–orbit coupling. Some critical points at which an accidental degeneracy of the SSs exist have been revealed. Near the critical points, negligible distortions can crucially change the SS. It is demonstrated that the ground SS of the pyramidal MeO 5 complex is very sensitive to the symmetry and magnitude of its distortions. SS diagrams in the parameter space'effective charge'–'distortion magnitude'have been established. It is revealed that the IS state exists as a ground state for all considered distortions with a corresponding choice of Z eff. Jahn–Teller distortions stabilize the IS state in a wide range of Z eff. The orbital-like reorientation of the electron density distribution was observed for the IS state at some threshold magnitude of Jahn–Teller distortions.