Amino acid-derived Schiff base complexes had been well explored as antimicrobial agents and the imidazole-based Heme oxygenase (HO) inhibitors were proposed as novel antimicrobial agents with a novel mechanism of action i.e., inhibition of microbial-HO, an enzyme essential for microbial survival in the human host. In line with this, we have synthesized and characterized three novel L-Histidine-based Schiff base derivatives (HKA-1,2 and 3) as inhibitors of microbial-HO. All the compounds were confirmed to be non-hemolytic and possess microbial-HO inhibitory activity against the microbial-HO's tested. HKA-1 showed good antimicrobial activity against Bacillus subtilis (6.25 µM), Escherichia coli (0.78 µM), Candida albicans (3.125 µM), and Saccharomyces cerevisiae (0.78 µM) whereas HKA-2 and HKA-3 showed good antimicrobial activity against Pseudomonas aeruginosa (3.125 µM) and Staphylococcus aureus (0.78 µM) respectively. According to molecular docking analysis, the HKA-1 with quinoline moiety showed better interaction with all the microbial HO's tested with a Glide Score extending from -9.71 to -5.51 Kcal/Mol whereas HKA-2 and HKA-3 with bi-phenyl moiety showed interaction with certain microbial-HO's with a Glide Score extending from -7.9 to -2.22 Kcal/Mol and -8.49 to -3.14 Kcal/Mol respectively. The formation of hydrogen bonds between ligand-protein interactions confirmed the stability of the complexes and the compounds reported in the present study could be used to treat drug-resistant pathogens.