A three-component Mannich reaction of different ketones with aromatic aldehydes and different amines in microwave irradiation under solvent free condition afforded corresponding β-amino carbonyl compounds in excellent yields. This method proved as a novel and improved modification of the reported three-component Mannich reaction in terms of milder reaction conditions, reaction times, clean reaction profiles, very small quantity of catalyst and simple workup procedure. Newly synthesized β-aminoketones were characterized by spectral studies. Structure of compound 4a was also confirmed by single-crystal X-ray analysis. All the compounds were screened for their antimicrobial activity by MIC method. Few of the molecules were found to be biologically potent.