In order to protect apple trees against scab, powdery mildew and post-harvest diseases, a large number of fungicides are applied in apple orchards from green-tip stage to harvest. To satisfy society’s demand to decrease the number of plant protection treatments, innovative protection strategies were assessed over four years in experimental orchards. In the case of apple scab, fungicide protection management takes the primary inoculum level and the means for reducing this inoculum, as well as the cultivar susceptibility, into account, in order to define a climatic risk level (according to Mills) as the intervention threshold. The decision to use fungicides against powdery mildew is based on the assessment of disease levels present in the orchard (use of a percentage threshold of leaves infected with powdery mildew). The application of these decision rules makes it possible to reduce the number of fungicide applications against scab and/or powdery mildew by more than 50%, while keeping these two diseases under control. In organic farming systems, the cultivar most susceptible to scab had scab damage on fruits despite careful reduction of the inoculum at fall and a large number of fungicide treatments during the season. No fungicide protection treatment for post-harvest diseases was applied in organically grown orchards nor in the low-input system for the two cultivars considered not to be highly susceptible to these diseases. These different protection strategies are assessed in terms of disease control and economic costs.