There is limited data regarding the specific problems faced by organic fruit growers when dealing with plant protection, particularly at a European Union level, though some general knowledge about pest and disease incidence can be found. Such information is crucial to improve the efficacy of a targeted knowledge transfer to organic fruit growers and advisors aiming at an increased adoption of innovative practices. A survey was thus carried out in seventeen European countries (16 EU member states and Switzerland), within the framework of the EU-funded project BIOFRUITNET, aiming at filling this knowledge gap also in terms of research needs. A questionnaire including a section about general aspects of orchard management (functional biodiversity, fertilization management, varietal/rootstock selection) and a section specifically dedicated to pest and disease occurrence and management in organic orchards was utilized to interview about 250 professionals (farmers and advisors), 155 of which were involved in pome fruits (including apple and pear) production. The analysis of the answers related to plant protection pointed out a varied situation about pest and disease occurrence in apple and pear orchards across Europe, though related to the zonal location of the respondent. However, more than 50% of respondents generally considered just few among the most damaging ones, normally co-occurring in the orchards. Interestingly, regardless of the respondents’ nationality or zonal location, more pests than diseases were indicated as relevant agents threatening organic pome fruits production. Nevertheless, only few measures promoting functional biodiversity in the orchards resulted in being broadly implemented in all regions. The analysis of the data underlines the strong demand for the development of a toolbox of measures that can be integrated successfully into the general orchard management strategy including the successful enhancement of functional or general biodiversity.