Solanum glycoalkaloids are gaining increased scientific attention due to their bioactive potential in the defense of plants against pests and pathogens. The comprehensive glycoalkaloid profiling from the leaves, stems, and roots of seven underexploited Solanum species (S. caripense, S. melanocerasum, S. muricatum, S. nigrum, S. quitoense, S. retroflexum, and S. sisymbriifolium) was conducted using high-performance liquid chromatography–time-of-flight mass spectrometry. A total of 51 glycoalkaloids were shared among the studied Solanum species, with concentrations ranging from 7 to 5.63 × 105 ng g−1. Based on the glycoalkaloid composition, plants were separated into two clusters, Cluster 1 (S. melanocerasum, S. nigrum, and S. retroflexum) and Cluster 2 (S. caripense, S. muricatum, S. quitoense, and S. sisymbriifolium). The inhibition activity of glycoalkaloid extracts on acetylcholinesterase showed a half-maximal inhibitory concentration (IC50), ranging from 0.4 (S. nigrum stems) to 344.9 µg mL−1 (S. sisymbriifolium leaves), that was not directly correlated to the total glycoalkaloid contents. This suggests that the composition of glycoalkaloids in the plant extract, rather than the total concentration, is a driver of biological activity. The study provides a framework for the bioprospecting of underexploited Solanum species for exploring bioactive glycoalkaloids and other compounds with potential pesticidal activities for the development of green bioformulation. This is the first comprehensive report on the glycoalkaloid profiles of S. retroflexum.