The use of resistance inducers is a promising development in the management of plant diseases, owing to their ability to control a broad spectrum of pathogens and improve the efficacy of fungicides. This study evaluates different sources of phosphonates (potassium, manganese, copper), a formulation prepared from the by‐products of the coffee industry (Greenforce CuCa), as well as the effects of their application, alone or in association with fungicide, in the management of two important coffee fungal diseases in Brazil: leaf rust and brown eye spot, caused by Hemileia vastatrix and Cercospora coffeicola, respectively. The effect of these products on defoliation, productivity and chemical composition of coffee beans (content of trigonelline, chlorogenic acid, caffeine and total soluble solids) was evaluated. Among all the alternative products tested individually, potassium phosphonate (P2O5—33.6% + K2O—29%) stood out, particularly for rust control, which was similar to the results of fungicide treatments. Treatments with fungicide, Greenforce CuCa and cuprous oxide, individually, caused less plant defoliation. Regarding the chemical composition of the coffee beans, the manganese phosphonate treatment showed the highest values for trigonelline, chlorogenic acid, caffeine and total soluble solid content. The results of this study show that resistance inducers can be useful in disease management, may come to eventually replace traditional fungicides and can also contribute to the beverage quality.