One pot reaction mixture of Salicylaldehyde, furfural amine, and further addition of cis-[MoO2(acac)2] in ethanol yielded cis-[MoO2L2] type complex, cis-[MoO2(Sal-Fa)2], where Sal-Fa stands for the deprotonated condensate of salicylaldehyde and furfural amine, (2-[(E)-{[(oxolan-2-yl)methyl]imino}methyl]phenolate). The yellow-colored crystals obtained by slow evaporation of the reaction mixture were used to collect single-crystal X-ray diffraction data, and the structure of the complex was elucidated. Further, the complex, cis-[MoO2(Sal-Fa)2], was characterized by various spectroscopic techniques such as FTIR, UV-visible, 1H-NMR, and 13C-NMR. The results were consistent with the molecular structure determined by single-crystal X-ray diffraction data. The cyclic voltammogram of the complex shows an irreversible one-electron reduction response at − 1025 mV for the Mo(VI) to Mo(V) reduction. cis-[MoO2(Sal-Fa)2] shows antibacterial activity against Staphylococcus sp (Gram-positive bacteria) and Klebsiella (Gram-negative bacteria). The minimum inhibitory concentrations were 5 mg/mL and 7.5 mg/mL, respectively. Furthermore, molecular docking studies against Glucosamine-6-phosphate synthase (GlcN-6-P), a crucial bacterial and fungal enzyme target, showed an excellent binding free energy of -9.02 kcal/mol, where the standard antibiotic streptomycin binding free energy is -5.72 kcal/mol. These findings highlight the potential of furan-based Schiff-base molybdenum complexes as scaffolds for developing new therapeutic agents with enhanced biological activity.