Two multi-component coordination compounds of Mn(II), viz. [Mn(H2O)6](2-Mepy)2(4-NO2bz)2·2H2O (1) and [Mn(H2O)6][Mn(2,3-PDCH)3]2 (2) (where, 2-Mepy = 2-methylpyridine, 4-NO2bz = 4-nitrobenzoate, 2,3-PDC = 2,3-pyridinedicarboxylate), have been synthesized and characterized using elemental, spectroscopic (FT-IR and electronic), TGA and single-crystal X-ray diffraction analyses. Complex 1 is a co-crystal hydrate of Mn(II) involving uncoordinated 2-Mepy, 4-NO2bz and water molecules; while compound 2 is a multi-component molecular complex salt of Mn(II) comprising cationic [Mn(H2O)6]2+ and anionic [Mn(2,3-PDCH)3]−complex moieties. The uncoordinated 2-Mepy and 4-NO2bz moieties of 1 are involved in lone-pair (l.p)-π and C–H⋯π interactions which stabilize the layered assembly of the compound. The crystal structure of compound 2 has been previously reported. However, we have explored the unusual enclathration of complex cationic moieties within the supramolecular host cavities formed by the molecular assembly of complex anionic moieties. The supramolecular assemblies obtained in the crystal structure have been further studied theoretically using DFT calculations, quantum theory of atoms-in-molecules (QTAIM) and non-covalent interaction plot (NCI plot) computational tools. Theoretical studies reveal that the combination of π-staking interactions (l.p-π, π-π and C–H···π) have more structure-guiding roles compared to the H-bonds. The large binding energy of π-stacking interactions in 2 is due to the antiparallel orientation of aromatic rings and their coordination to the metal centers, thereby increasing the contribution of the dipole–dipole interactions.