Abstract Grapevine ( Vitis vinifera ) is one of the most important fruit crops, but it is susceptible to several pests and pathogens. Pesticide applications are required to prevent yield and quality losses, and fungicides represent the largest fraction of treatments in plant protection programs under conventional, integrated, or organic disease management. Thus, alternative fungicides are being developed for the sustainable control of grapevine pathogens, such as biocontrol agents and natural products. In addition to toxicological and ecotoxicological tests, there is considerable interest in verifying possible effects of plant protection products on non‐target microorganisms. This review highlights recent advances in understanding the impact of plant protection programs and alternative fungicides on the taxonomic composition of bacterial and fungal communities of the grapevine phyllosphere. Amplicon sequencing studies revealed that the grapevine microbiota is primarily shaped by the plant compartment, vineyard location, and sampling time. Plant protection programs generally have only a minor impact on the taxonomic composition of microbial communities on grapevine bunches, leaves, and wood, suggesting the resilience of indigenous phyllosphere microorganisms. However, the effects of fungicide treatments can vary with fungicide dosage, application frequency, grapevine cultivar, and environmental conditions, indicating that further long‐term studies with more frequent applications are required to clarify the effects of chemical and biological treatments on non‐target microorganisms at different sampling times.