Abstract In plants, the presence and distribution of specialized metabolites during the early stages of development are not documented enough, even though their biosynthesis is one of the most important strategies for survival. In this study, five alkaloids and four acetogenins were detected in Annona muricata L. during early development seedling, including three phases of root emergence and three of seedling formation. Hexane and alkaloid extracts were obtained from each organ, which were analyzed in a gas-mass chromatograph and in a high-performance liquid chromatograph coupled with a photodiode array UV detector (HPLC-DAD). This research shows the presence of the acetogenins cis-uvarimicin IV, mosinone, muricina B, and cis-annonacin-10-one, as well as of the alkaloids reticuline, coreximine, anonaine, asimilobine, and nornuciferine, both groups with a variable organ-specific distribution, related with the formation of organs and tissues.