Mn(II) and Co(II) complexes of methyl‐(Z)−N′‐carbamothioylcarbamohydrazonate Schiff base ligand were synthesized. The ligand and metal salts were taken in 2 : 1 stoichiometric ratio. All the synthesized complexes were characterized using elemental analysis, molar conductance, magnetic moment and various spectroscopic techniques (FT‐IR, UV/VIS, EPR) techniques. Elemental and spectroscopic results verified bidentate donor nature of the ligand and octahedral geometry of all the complexes. The non‐electrolytic nature of Mn(II) and Co(II) complexes were suggested by conductivity data analysis. In vitro antibacterial (E. coli and S. aureus) and antifungal (C. albicans and C. tropicalis) screening were achieved by employing agar well diffusion method which revealed better antimicrobial activity of Co(II) complexes than Mn(II) complexes. In silico SwissADME study predicted the drug‐likeness probability of ligand and complexes. The interaction of two bacterial proteins (E. coli and S. aureus) with compounds was also analyzed using molecular docking study, which corroborate the in vitro analysis.