Density functional theory (DFT) and dispersion-corrected DFT calculations were used to study the nature of Mn≡E bonds in the cationic manganese-ylidyne complexes trans-[H(dmpe)2Mn≡E(Mes)]+ (E = Ge, Sn) and [H(dmpe)2Mn≡Sn(C6H3-2,6-Mes2)]+ by using BP86, PBE, and PW91 functionals. The calculated geometrical parameters of the stannylidyne complexes are in good agreement with the available experimental values. Significant non-covalent interactions appear between the metal fragment and the ligands in the studied complexes, which were determined by the QTAIM-defined topological analysis. The electronic structure of the Mn≡E bonds was examined by Voronoi deformation density (VDD) charges and Nalewazskii–Mrozek bond orders. The overall electronic charge transfers from [E(Mes)] or [E(C6H3-2,6-Mes2)] to [H(dmpe)2Mn] fragment. The energy decomposition analysis shows that the Mn≡Ge bond has more covalent character than ionic, and the percentage of ionic character increases from Ge to Sn. The bond dissociation energy at the DFT/BP86 level for the Mn≡Ge bond (67.6 kcal/mol) is larger than that of the Mn≡Sn bond (55.8 kcal/mol). The D3(BJ) dispersion interactions between metal fragment and EMes ligands add nearly 17.0 kcal/mol to the Mn≡E bond dissociation energies. The dispersion energy contribution increases with the bulkiness of the ligand substituent. The distortion of the Mn–E–C bond angle has been discussed in terms of a Jahn–Teller distortion.