The coca family (Erythroxylaceae) consists of trees and shrubs sub-divided into four genera: Aneulophus, Nectaropetalum, Pinacopodium, and Erythroxylum, which include species with highly valuable medicinal compounds. E. delagoense, E. emarginatum, and E. pictum are endemic to southern Africa and have great pharmaceutical potential based on their traditional uses. Previous studies have shown certain inconsistencies in terms of the presence or absence of tropane alkaloids in these species, resulting in a need for further research and clarification. Therefore, the aim of this study was to determine the seasonal variation of the immediate biosynthetic precursor of cocaine, the tropane alkaloid, ecgonine methyl ester in the three South African Erythroxylum species by means of gas chromatography–mass spectrometry, as well as to conduct a phytochemical screening for observing the presence of other potential compounds and tropane alkaloids. We found significant differences in tropane concentrations from the seasonal variation study, explaining the discrepancies in previous reports on its presence/absence in these species. Furthermore, we report for the first time on the occurrence of selected highly valuable tropane alkaloids in E. emarginatum currently used in ‘blockbuster medicine’.