Two new metal–organic multi-component compounds of Ni(II) and Co(II), viz. [Ni(3-CNpy)2(H2O)4]ADS·2.75H2O (1) and [Co(3-CNpy)2(H2O)4](4-ClbzSO3)2 (2) (3-CNpy = 3-cyanopyridine, ADS = anthraquinone-1,5-disulfonate, 4-ClbzSO3 = 4-chlorobenzenesulfonate), were synthesized and characterized using single crystal XRD, TGA, spectroscopic (IR, electronic) and elemental analyses. Both the compounds crystallize as multi-component compounds of Ni(II) and Co(II), with uncoordinated ADS and 4-ClbzSO3 moieties in the crystal lattice, respectively. Crystal structure analyses revealed the presence of antiparallel nitrile···nitrile and π-stacked assemblies involving alternate coordinated 3-CNpy and uncoordinated ADS and 4-ClbzSO3 moieties. Moreover, unconventional charge reverse Cl∙∙∙N halogen bonding contacts observed in compound 2 provide additional reinforcement to the crystal structure. Theoretical calculations confirm that the H-bonding interactions, along with anion–π(arene) and anion–π(CN) in 1 and π–π, antiparallel CN···CN and charge reverse Cl···N halogen bonds in 2, play crucial roles in the solid state stability of the compounds. In vitro anticancer activities observed through the trypan blue cell cytotoxicity assay reveal that the compounds induce significant concentration dependent cytotoxicity in Dalton’s lymphoma (DL) cancer cells, with nominal effects in normal healthy cells. Molecular docking studies reveal that the compounds can effectively bind with the active sites of anti-apoptotic proteins, which are actively involved in cancer progression.