An efficient microwave assisted protocol for the exclusive one pot synthesis of N-amino-methyl substituted 1,4- benzodiazepine derivatives 4(a-f) and 5(a-f) by the reaction of N-amino-methyl substituted isatoic anhydride 1(a-f) with glycine and L-proline respectively has been described. Treatment of N-amino-methyl substituted isatoic anhydride 1(a-f) with amino acids glycine and L-proline afforded 4(a-f) and 5(a-f) respectively in excellent yield. The derivatives of N-aminomethyl substituted 1,4-benzodiazepine 4(a-f) and 5(a-f) were screened for their in-vitro antimicrobial activities against bacterial species (E.coli and B.subtilis) and fungal species (A.niger and A.flavus) by Agar-well assay method against the standard drugs (ciprofloxacin for bacteria and fluconazol for fungi).