The local structures and spin Hamiltonian parameters (SHPs, g factors, and hyperfine structure constants) for the Cu(en)32+ and Ru(en)33+ clusters in ethylenediamine complexes are theoretically studied from perturbation formulae for tetragonally and trigonally elongated octahedral 3d9 and 4d5 clusters, respectively. Cu2+ centres I and II may experience the slight relative elongations ΔZ by about 0.005 and 0.007 Å in Zn(en)3(NO3)2 polycrystalline powder at 4.2 K and room temperature, respectively, along the C4 axis arising from the Jahn–Teller effect. For Ru(en)33+ cluster in the uniaxial [Rh(en)3Cl3]2NaCl ⋅ 6H2O single crystal doped with the single-crystal chloride salt [Ru(en)3]Cl3 ⋅ 4H2O, the local impurity–ligand bonding angle related to the C3 axis suffers a negative variation Δβ (≈−1.85°) with respect to the host βH in [Ru(en)3]Cl3 ⋅ 4H2O at 4 K. The features of SHPs and defect structures for the Cu(en)32+ and Ru(en)33+ clusters are also discussed in view of the different experimental temperatures.