The Cape Floristic Region (CFR) is renowned for its rich biodiversity and high levels of endemism, leading to its designation as a UNESCO World Heritage Site in 2004. Despite its ecological significance, the region’s poor soils, characterized by low nitrogen and phosphorus content, raise questions about how its flora thrives under such conditions. Research indicates that plants adapt to stress by producing secondary metabolites, particularly phenolic compounds, vital for ecosystem functioning, including nutrient cycling and defense against stressors. Furthermore, low biological decomposition rates in nutrient-poor soils suggest that fire is crucial in litter breakdown and nutrient release, influencing plant health. Our study employed leaf spectroscopy to examine the relationship between phenolic compounds (total phenol and flavonoid) and post-fire recovery across the CFR. Results show that fire rejuvenates this ecosystem, with high concentrations of phenolic compounds found in areas recently affected by fire (2015, 2016, and 2021). In contrast, limited (2010) or no recent fire (“never_exp”) resulted in significantly lower concentrations of phenolic compounds. Additionally, continuum removal was employed on the leaf spectra to improve the detection of subtle absorption features associated with phenolic content. Our findings indicate that the prediction of total phenols (R² = 0.82, NRMSE = 5.98%) was generally more accurate than that of flavonoids (R² = 0.80, NRMSE = 1.36%), with total phenols estimated using short-wave infrared (SWIR) spectra. This study enhances the understanding of the absorption features of phenolic compounds in the CFR.