NHC-containing compounds are well known for their diverse and promising bioactivities. Incorporation of a metal center into a heterocyclic framework can significantly enhance the bioactivity, leading to improved efficiency. In this scenario, three new bi-imidazolium salts (ZS1-ZS3) and their respective organoselenium compounds (ZC4-ZC6) were synthesized and characterized using various techniques, including UV-visible, FTIR and FT-NMR (1H and 13C) spectroscopy. Synthesized adducts were evaluated for their antimicrobial efficacy against different bacterial and fungal strains. Surprisingly, the test compounds demonstrated good antibacterial and antifungal activity with ZI values (12.12 to 22.15 mm), (10.11 to 28.01 mm) and (16.95 to 23.67 mm) against E. coli, S. aureus and A. niger, respectively. Compounds ZC6, ZS3 and ZS2 exhibited comparatively strong inhibition, with MIC values of (10.78 ± 0.08 μM) against E. coli, (9.43 ± 0.11 μM) against S. aureus and (9.12 ± 0.10 μM) against A. niger. Notably, Se-NHC adducts demonstrated significantly enhanced cytotoxic effects against HCT-116 and MCF-7 cancer cell lines compared to the corresponding NHC-salts, which substantiates the contributory role of selenium in improving the bioactivity of these compounds. Among the test compounds, ZC5 exhibited significantly higher cytotoxicity than the standard drug 5-FU (P < 0.001, ANOVA followed by Tukey's post hoc test), with IC50 values of (1.57 ± 0.04 μM) and (1.63 ± 0.07 μM) against HCT-116 and MCF-7, respectively.