Sibiya, Sihle BCho, Moses AMutanga, OOdindi, JMasemola, CeciliaVan Staden, JVambe, M2026-09-072026-09-072026-081366-59010143-1161https://doi.org/10.1080/01431161.2026.2719401http://hdl.handle.net/10204/14928Fire is a key physical driver of ecosystem change, while plants rely on secondary metabolites such as phenolic compounds for chemical defense. Despite their importance, fire effects on secondary metabolites are often studied separately. Consequently, the mechanisms by which post-fire conditions shape the levels and diversity of secondary compounds in plant communities remain poorly understood. In this study, we used leaf spectroscopy to investigate how post-fire affects secondary metabolites in the fire- driven fynbos biome, a system rich in secondary metabolites. Results showed that both fire and secondary metabolites contribute to ecosystem rejuvenation. Areas subjected to recent fires in 2015, 2016, and 2021 exhibited high phenolic levels, whereas regions with limited fire in 2010 or no recent fire (“never_exp”) had low phenolic concentrations. Using continuum removal, we identified the strongest spectral features for total phenols at 1660 nm and for flavonoids at 415 nm. Because chlorophyll also absorbs strongly in the 410–430 nm region, we evaluated and adjusted multiple spectral indices to improve flavonoid sensitivity. The Flavonoid Index (FI)415,710 and FI420,710 showed the strongest relationships with phenolic content (R flavonoids: R 2 = 0.55; RRMSE ≈ 1.98– 1.99%). Phenolic concentrations were also estimated using random forest regression. Prediction of total phenols was generally more accurate than flavonoids (total phenols: R 2 2 = 0.82, RRMSE = 12.54%; = 0.81, RRMSE = 10.75%). Total phenols were best modeled using short-wave infrared (SWIR) spectra, while flavonoids were best modeled using full (VSWIR) spectra. Overall, our findings clarify the coupled roles of fire and secondary metabolites in supporting fynbos resilience and regeneration.FulltextenPhenolic compoundsTotal phenolFlavonoidHyperspectral remote sensingFynbos biomeArticlen/a