Stip is a physiological disorder that affects certain pepper (Capsicum annuum) cultivars, most notably bell-pod types. It has been attributed in the literature to nutrient imbalances, temperature extremes, and/or other environmental stressors. Symptoms present as brown, black, and yellow ovoid-shaped necrotic lesions ≈0.5 to 1.2 cm long by 0.5 cm wide. Between 2014 and 2015, symptomatic and asymptomatic pods were harvested from 15 commercial farms in southern New Mexico. Fluorescent microscopy comparisons of harvested symptomatic tissue revealed a unique fluorescent signature and the absence of chlorophyll. A new spectral peak centered around 560 nm was observed in symptomatic tissue. High-performance liquid chromatography (HPLC) and gas chromatography–mass spectrometry (GC-MS) analyses of these tissues detected significant differences in 13 metabolites, of which several have been associated with fruit maturation and/or senescence. This report represents the first combination of a detailed microscopic description and metabolite profile of field-grown symptomatic plants with this disorder.