Annona purpurea grows in the areas of low elevation in deciduous forests of Mexico, those areas have marked rainy and dry seasons. This species produces more than 30 bioactive alkaloids that could have potential in the control of phytopathogens. This research provides data on the variation of the content and number of alkaloids during an annual cycle and the associated inhibitory potential of the compounds against three phytopathogenic fungi. For one year, alkaloidal extracts of stems and leaves were obtained every two months. The extract profiles were determined by gas chromatography with tandem mass spectrometry and their antifungal activity was examined in vitro. The alkaloids, annomontine and oxopurpureine, obtained from the roots and leaves, respectively, were also evaluated individually. The yields, profiles and activities of the extracts, as well as the abundance of annomontine and oxopurpureine in the extracts, were contrasted with the seasonality and phenological phases of the plant. The data indicate that the alkaloid content was higher at the height of the dry season. High yields also occurred during flowering. The strongest inhibitory effect was obtained from the root extracts during the last month of dry season. This finding seems to be explained by the higher chemodiversity of alkaloids in extracts from this season. Annomontine and oxopurpureine inhibited all three phytopathogens; however, they were not solely responsible for the activity of A. purpurea.