A series of novel highly functionalized benzoylaminocarbothioyl pyrrolidines were prepared from benzoylisothiocyanate and substituted pyrrolidines in excellent yield. The crystal structure of the novel 1-benzoylaminocarbothioyl-5-(naphthyl)-pyrrolidine-2,3,4-tricarboxylicacid trimethyl ester (3a) was determined by X-ray crystal structure analysis. The synthesized compounds were characterized and screened for their in vitro antibacterial and antifungal activities and toxicity. The prepared compounds were tested against the standard strains: Escherichia coli (ATCC 25922), Enterobacter cloacae (ATCC 13047), Enterococcus faecalis (ATCC 29212), Pseudomonas aeraginosa (ATCC 27853), Staphylococcus aureus (ATCC 29213) and Staphylococcus epidermidis (ATCC 12228) and the yeasts Candida albicans (ATCC 90028), Candida krusei (ATCC 6258), Candida parapsilosis (ATCC 22019), Candida tropicalis (ATCC 22019) and Candida glabrata (ATCC 32554).