Abstract Pesticides constitute a major threat to biodiversity, but our understanding of the complex interactions between local and landscape factors influencing their distribution in agroecosystems remains limited. We conducted a pioneering study where we screened spiders, rodents, plants and soils for multiple pesticide residues in perennial crops (orchards and vineyards) managed under organic (N = 8) and integrated pest management (N = 8) systems. We then quantified the proportional representation of major habitat types in surrounding landscapes. Additionally, we conducted interviews with farmers to gain precise insights into pesticide applications. We expected that landscape factors would be more important for mobile entities (i.e. spiders and rodents), while management type would be relatively more important for the sedentary entities (i.e. soils and plants). We detected various pesticides within studied crop types, including several forbidden in the European Union. We found that pesticide distribution in spiders was influenced by the proportion of semi‐natural habitats in the landscape, with pesticide concentration decreasing as the proportion of semi‐natural habitats increased. Additionally, we observed that the spectrum of pesticides in spiders increased with the dominance of web‐building spiders. In contrast, pesticide levels in rodents were not affected by either landscape composition or local management type. For plants, pesticide distribution was affected by the proportion of forests and shrublands and, to some extent, by local management practices. In the case of soil, pesticide distribution was primarily determined by local management. This study marks an effort in demonstrating that both local and landscape factors play crucial roles in shaping pesticide distribution within perennial crops. Importantly, the relative importance of these factors varied across the four matrices investigated. Synthesis and applications: To comprehend the factors that determine pesticide distribution in crops, it is crucial to monitor diverse ecosystem components rather than focusing on a few model species. This approach underscores the necessity for ecologically sensitive management at landscape scale. Such management should involve the preservation and enhancement of (semi)natural habitats around crops. These combined insights can form the foundation for conservation and management initiatives aimed at mitigating the impact of pesticides on biodiversity within crops.