BACKGROUND Solanum scabrum berries in sub‐Saharan Africa are prolific but neglected as an agricultural resource. Recognition and application of such underutilized resources rely on systematic study of the relevant phytochemicals of commercial value. RESULTS The quantities of a total of 54 phytochemicals in Solanum scabrum berries were assessed using HPLC‐MS methods. Berries from eight different genetic sources were analyzed with two entries monitored across different maturation stages. There was a significant variation among mature berries in the accumulation of phenolic acids, 91.5–794 mg·100 g−1 dry weight (DW); flavonols, 76.3–897 mg·100 g−1 DW; anthocyanins, 178–4650 mg·100 g−1 DW; glycoalkaloids, 1.76–1630 mg·100 g−1 DW; and saponins, 82.2–606 mg·100 g−1 DW. Fruit development from immature to post‐frost harvest featured dynamic changes in phytochemical composition and, despite remarkable differences in the absolute magnitude of content, the trend of change was generally similar in different genetic sources. CONCLUSIONS The genotype‐dependent difference in toxic glycoalkaloids in mature berries may partially explain the consumption controversy as it reflects glycoalkaloid content. The analytical methods applied in this work should serve for quality control of glycoalkaloids thereby improving the safe utilization of this berry. In addition, the selection and breeding of new genotypes with low and safe levels of glycoalkaloids and saponins in the berry could be of value in sub‐Saharan Africa to increase nutrition and generate new income opportunities for growers.