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Two new metal complexes of general formula M(Haαft)2 [M = NiII and CuII] of asymmetrical Schiff base ligand (HL = Haαft) derived from amoxicillin and α-formylthiophene have been prepared and characterized by various physicochemical and spectral techniques. Molar conductance measurement indicates nonelectrolytic nature of the metal complexes. FT-IR spectral study reveals the ligation of metal ions at two different nitrogen [NN] donor sites of Haαft. FT-IR and electronic absorption spectral evidences suggest distorted tetrahedral and square planar geometry for CuII and NiII complexes, respectively. The structure optimization by molecular mechanics (MM) force field calculation through ArgusLab 4.0.1 version software also supports the concerned geometry of the complexes. The cell dimensions as suggested by XRPD study, a (6.753 Å), b (13.904 Å), c (20.122 Å), α (142.76°), β (106.580°), and γ (72.4343°) for CuII and a (24.2547 Å), b (6.6371 Å), c (5.5047 Å) (α = β = γ = 90°) for NiII complexes, are in good agreement with their triclinic and orthorhombic crystal systems. Particle size calculation by Scherrer’s formula indicates nanocrystalline nature of the complexes. The antibacterial sensitivity study suggests promising activities of Haαft (Ligand) and M(Haαft)2 complexes against four clinical pathogenic bacteria, namely, E. coli, P. vulgaris, P. aeruginosa, and S. aureus, though being less active than the standard drug amikacin.