In the current work, a ligand N'1-((E)-2-hydroxy-3H-indol-3-ylidene)-N'3-((E)-2-oxoindolin-3-ylidene)malonohydrazide (H4MDI) and its chelates [Cr2(H2MDI)(H2O)2Cl4] and [Ni2(MDI)(H2O)6].4H2O have been isolated and characterized using different physico‐chemical methods, as infrared (IR), thermogravimetric analysis (TGA) and differential thermogravimetry (DTG) in the solid state, and 1H‐NMR, 13C‐NMR and UV/visible in solution. For evaluating the geometries for the synthesized ligand and its complexes, calculations were performed using Gaussian 9 program with density functional theory (DFT). Magnetic and UV/visible measurements proposed that both Cr(III) and Ni(II) chelates have octahedron coordination frameworks. On the other hand, the IR spectral data revealed that the ligand behaves as a binegtive hexadentate in [Cr2(H2MDI)(H2O)2Cl4] and as a tetranegative hexadentate in [Ni2(MDI)(H2O)6].4H2O. The molecular modeling was done, and illustrated bond lengths, bond angles, molecular electrostatic potential, and chemical reactivity for the inspected compounds. In addition, the behavior of thermal decomposition for prepared complexes was discussed. Two comparable methods (Coats-Redfern and Horowitz-Metzger) were used to calculate the kinetic parameters of the resulted thermal decomposition stages. Furthermore, the ion-flotation process was used for the separation of Ni(II) from aqueous media via the prepared ligand as a chelating agent and oleic acid as a surfactant. Moreover, the antimicrobial behavior of the synthesized moieties was investigated against various bacterial and fungal strains. H4MDI has the most pronounced activity with minimum inhibitory concentration (MIC) of 0.78 µg/mL for both E. coli, and C. Albicans, while Ni(II) complex shows the activity against S. aureus, E. coli, and C. Albicans with MIC of 3.42, 6.84, and 1.71 µmol/L, respectively. Finally, the in-vitro cytotoxic activity of the prepared compounds against human hepatocellular carcinoma cells (HePG-2) has been examined, and the obtained results revealed that H4MDI and its Ni(II) complex show an average activity against HePG-2 with IC50 of 9.7 and 7.7 µmol/L, respectively compared with the 5-flurouracil (applied standard drug) with IC50 = 7.9 µmol/L.