Universities in biodiversity-rich countries hold a strategic advantage for advancing plant biochemistry research on local and endemic species. Local plants are sources of unique secondary metabolites, nutritional compounds, enzymes, and bioactive molecules that can support innovations in health, agriculture, food systems, and sustainable materials. At the same time, research on local plant biochemistry faces persistent constraints: complex access and benefit-sharing (ABS) governance under the Nagoya Protocol, gaps in taxonomy and voucher practices, high chemical variability across seasons and sites, limited access to advanced instrumentation (LC–MS/MS, NMR, metabolomics), and challenges in standardization and reproducibility. This article provides a framework synthesis (≤2024) on local plant biochemistry research in higher education, focusing on the coupled challenges and opportunities that shape research quality and societal value. We integrate literature on plant metabolomics and standards (Fiehn, 2002; Sumner et al., 2007; Fernie & Tohge, 2017), natural products and dereplication workflows (Wolfender et al., 2019), ethnobotany and bioprospecting ethics (Heinrich et al., 2020), biodiversity governance and ABS (CBD, 2011; Oberthür & Rosendal, 2014), and sustainability-oriented translation (green extraction, life-cycle thinking, and cultivation–conservation linkages). Results are presented as two conceptual figures (a workflow from prioritization to sustainable scaling and a challenge–opportunity matrix), and three tables mapping (1) methodological approaches, (2) common challenges with mitigation strategies, and (3) opportunity pathways and institutional actions. We argue that local plant biochemistry research is most impactful when universities treat governance readiness, taxonomy rigor, FAIR metadata, and reproducible analytical pipelines as first-class research outputs—paired with partnerships for cultivation, standardization, and responsible commercialization. The paper concludes with an institutional roadmap that enables universities to build credible, ethical, and scalable local plant biochemistry programs while protecting biodiversity and community rights.