A series of antibacterial active pyranopyrazole-napthaquinone hybrids are synthesized from one pot condensation of sulphonated β-keto ester, simple β-keto ester, aromatic aldehyde, hydrazine in presence of piperidine catalyst under ethanol solvent conditions and subsequent replacement of SO2Ph group with 2-hydroxy naphthoquinone. We have conducted Structure Activity Relationship (SAR) studies based on initial antimicrobial screening of a set of twenty three conjugates against four bacterial strains (Bacillus subtilis, Escherichia coli, Staphylococcus epidermidis and Proteus vulgaris) and five antifungal stains (Aspergillus flavus, Monascus purpureus, Aspergillus niger, Penicillium citrinum and Candida albicans). SAR studies revealed that compounds 11d, 11e, 11r, 11s, 11t, 11u, 11v were found to be more active in antimicrobial screening. Anti-proliferative properties were evaluated against Du145, A549, FaDu human cancer cell lines. Among the derivatives MeO and CF3 substituted hybrid molecules 11r, 11s, 11t, 11u, 11v showed most potent cytotoxic activity against all four cancer cell lines.