Native corn in Cherán, Michoacán, southwestern Mexico, represents a high-impact economic, social, and religious support, although its yield is low due to fungal diseases. Fungicides are mainly used for their control, but the fungi involved create resistance. The aims of this study are to determine the incidence of foliar diseases in the field, isolate the causal fungi, evaluate the in vitro effect of the essential oil of rue (Ruta graveolens) on them, and identify the secondary metabolites. The essential oil was obtained using the steam distillation technique on fresh plants. Also used was an industrial-grade chitosan, and the commercial fungicide benomyl was used as a positive control. Rue essential oil was characterized by mass spectrometry with ultra-high-performance liquid chromatography with electrospray ionization (UHPLC-ESI). The highest incidence of disease was obtained for leaf rust (35%), followed by gray leaf spot (GLS) (24%) and leaf blight (19%). Rue essential oil inhibited 100% of the mycelial growth of Coniothyrium phyllachorae and 96% of the mycelium of Exseroilum turcicum. The benomyl fungicide effectively inhibited C. phyllachorae (86 to 91%), but not E. turcicum, with the opposite effect when using chitosan by inhibiting 89 to 90% of the latter’s mycelial development. The majority compound of the essential oil of R. graveolens was 2-(3-phenylprop-2-enoyl)chromen-4-one; however, fatty acids were also detected: linoleic, palmitic, and retinoic acid.