Secondary metabolites (SM) in plants play crucial pharmacological, ecological, and nutritional roles for humans, wildlife, and livestock. Environmental Heterogeneity (EH) encompasses the variability of biotic and abiotic factors that influence biological responses of plant species. Advancements in remote sensing have enhanced the ability to assess plant functional traits more affordably and comprehensively by integrating spectral reflectance data with detailed plant metabolomics. However, studies investigating the relationship between EH—quantified using Rao’s Q heterogeneity index from remote sensing data—and SM diversity remain limited. Here, we present the first report demonstrating that the biotic component of EH, measured as Rao’s Q, is positively associated with SM diversity in mesquite pod extracts—higher Rao’s Q values correspond to greater SM diversity. Generalized additive models (GAMs) revealed that Rao’s Q contributed the most explanatory power, accounting for 21.2% of the deviance, compared to pod weight (13.7%) and pod length (2.03%). However, only the relationship between Rao’s Q and SM diversity was statistically significant (p = 0.029). The Rao’s Q index derived from remote sensing serves as a scalable proxy for identifying SM hotspots, facilitating the targeted discovery of regions with high pharmacological or nutritional value.