In the current study, four different bio-microcapsules designed for biomedical purposes were produced from sporopollenin, a highly durable and biocompatible natural polymer found in the exine layer of spores and pollen grains. Comprehensive physicochemical characterisation of these microcapsules using FTIR, TGA, and SEM confirmed the successful chemical modification and structural integrity of the functionalised microcapsules. The synthesized formulations were evaluated with comprehensive in vitro biological analyses, including antioxidant potential (DPPH and FRAP assays), antibacterial (against P. vulgaris, P. aeruginosa, E. coli, S. typhi, and S. aureus – MIC and MBC assays), and anticancer (against HCT116, MDA-MB-231, and THLE-2 cell lines - Alamar assay) activities. Among the tested candidates, the Sp-GE-B1 and Sp-GE-B2 formulations exhibited superior performance across all biological assays. Antibacterial evaluations revealed significant inhibitory effects, particularly for Sp-GE-B2 , with low MBC/MIC ratios (≤2.0), indicating a strong bactericidal mechanism rather than mere growth inhibition against E. coli and S. typhi . The functionalised microcapsules Sp-GE-B1 and Sp-GE-B2 exhibited the best antioxidant performance, with IC₅₀ values of 96.81 μg/mL and 46.65 μg/mL in the DPPH assay, 71.15 μg/mL and 60.65 μg/mL in the FRAP assay, respectively. Consistent with the antioxidant findings, the Sp-GE-B2 bio-microcapsule demonstrated superior anticancer efficacy by inducing marked cytotoxicity in HCT116 (IC₅₀: 61.78 μg/mL) and MDA-MB-231 (IC₅₀: 80.10 μg/mL) cancer cell lines, while maintaining a significantly higher IC₅₀ value against normal THLE-2 hepatocyte cells (IC₅₀: 92.15 μg/mL), indicating a favourable therapeutic index. Collectively, these results underscore the potential of structurally engineered sporopollenin-based microcapsules as multifunctional platforms for antioxidant, anticancer, and antibacterial applications, offering a promising avenue for the development of targeted and bioactive delivery systems.