Pharmaceutical materials science is shifting from synthetic nanotechnology toward naturally occurring micro-architectures. Sporopollenin Exine Capsules (SECs), derived from plant pollen, have emerged as promising candidates due to their evolutionary resilience and chemical stability. To evaluate their potential, a systematic review following PRISMA 2020 guidelines was conducted across Web of Science, Scopus, and PubMed (January 2015–July 2025). The screening process excluded agricultural and industrial applications to focus strictly on biomedical innovation, with risk of bias assessed using a modified Klimisch score for in vitro and preclinical studies. Of 2621 records, 51 original research articles met the inclusion criteria. Bibliometric analysis identified a research inflection point in 2014, marking a transition to applied materials science. Bio-sources have diversified beyond Lycopodium clavatum, with successful applications in oral drug delivery (n = 21), advanced biomedical targeting (n = 16), and material characterization (n = 14). Quantitative findings demonstrate loading efficiencies ranging from 3% to 79%, carrier sizes typically 10–75 μm, and tunable release kinetics engineered for targeted delivery. Overall, SECs demonstrate high biocompatibility, diverse loading capabilities, and functional advantages such as mucoadhesion. However, a “translational gap” remains between material characterization and clinical implementation. Future research must focus on standardized extraction protocols, comprehensive safety profiles, and clarification of regulatory pathways to enable clinical translation.