A protocol for managing the main diseases and pests of sweet cherry in Spain (New IPM) has been implemented in order to reduce the use of pesticides. This New IPM includes nonchemical strategies, such as biological products against diseases and mass trapping of pests, and adjusts the timing and number of pesticide applications according to damage thresholds and a predictive model of diseases based on climatic factors. The New IPM was compared—in commercial orchards from the main cherry-producing areas in Spain (Aragon and Extremadura)—to the integrated management usually carried out in these areas (Standard IPM). Furthermore, a multiresidue method for the determination of the residues in cherries was developed. The number of applications, active ingredients used, and residue levels in fruit were reduced very significantly with this New IPM without affecting the effectiveness in the control of the main cherry diseases (brown rot, shot-hole, and leaf-spot) and pests (European cherry fly, spotted wing drosophila, and black cherry aphid). Neither significant differences in the abundance and diversity of microorganisms in flowers and fruit nor soil and canopy dwelling arthropods were observed between the two protocols, although some positive effects of this New IPM were seen on some groups of natural enemies.