Soils act as sinks for many organic contaminants, posing a threat to biodiversity and essential ecosystem services. In this study, we assessed the contamination status of soils in 140 Important Bird and Biodiversity Areas (IBAs) in Spain. Fifty-two organic contaminants including organochlorine pesticides (OCPs), organophosphorus pesticides (OPPs), polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and plasticizers or plastic related such as phthalates, bisphenol A, nonylphenol, and organophosphate esters (OPEs) were analyzed by gas chromatography coupled to tandem mass spectrometry (GC-MS/MS). The mean soil concentration ranged from 1.41 to917ng/g and plasticizer and PAHs were detected at the highest concentrations, while OCPs were the most frequently detected. Hierarchical clustering on principal components (HCPC) and land use data associated PCBs with artificial land, phthalates with industrial sites and incineration plants and PAHs with burned areas, and in a lesser extent pesticides with agricultural activities. A tier I environmental risk assessment (ERA) was performed to identify the most impacted natural areas and the most concerning compounds. Out of the 140 IBAs, 95 presented at least one compound at high-risk concentrations (RQ > 1) for soil organisms. The OPPs chlorpyrifos and malathion, together with the PAH benzo[b]fluoranthene, were detected at high-risk concentrations. Overall, this study highlights the widespread presence of organic contaminants in areas of high natural value and the importance of implementing monitoring studies to identify potential contaminated sites that require conservation and remediation actions for the protection of biodiversity.