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Vanillin containing 9H-fluoren sulfone scaffolds were prepared by coupling a sulfone amine with carboxylic acid group of amino acids in presence of peptide coupling reagent hexafluorophosphate benzotriazole tetramethyl uronium (HBTU). All eight (6a–6h) synthesized vanillin containing 9H-fluoren sulfone scaffolds were evaluated for their biological activities, namely, antibacterial, antifungal and antimalarial. The antibacterial evaluation revealed that compounds 6b-6g exhibited potency against tested pathogenic bacteria, especially against Staphylococcus aureus. Compounds 6b, 6f and 6h manifested considerable antifungal activities against Candida albicans, Aspergillus niger and A. clavatus. Moreover, the antimalarial result demonstrated excellent antimalarial activities for compounds 6b and 6f against Plasmodium falciparum with IC50 less than the standard quinine. Further, molecular docking study was performed to find molecular level interaction of compounds with malarial drug target enzyme P. falciparum dihydrofolate reductase-thymidylate synthase (pfdher-ts). Interestingly, for all tested sulfone scaffolds the docking energy was found between −8.6 to −10.6 kcal/mol, which was higher than both of the standard drugs’ (quinine and chloroquine) docking energy, i.e. −8.4 and −6.9, respectively. The results of this study confirmed the importance of the sulfone class of compounds in the treatment of parasitic infections and microbial infections.