Plastic additives, such as phthalates, are ubiquitous contaminants that can have detrimental impacts on marine organisms and overall ecosystems' health. Valuable information about the status and resilience of marine ecosystems can be obtained through the monitoring of key indicator species, such as cetaceans. In this study, fatty acid profiles and phthalates were examined in blubber biopsies of free-ranging individuals from two delphinid species (short-finned pilot whale – Globicephala macrorhynchus, n = 45; common bottlenose dolphin – Tursiops truncatus, n = 39) off Madeira Island (NE Atlantic). This investigation aimed to explore the relations between trophic niches (epipelagic vs. mesopelagic), contamination levels, and the health status of individuals within different ecological and biological groups (defined by species, residency patterns and sex). Multivariate analysis of selected dietary fatty acids revealed a clear niche segregation between the two species. Di-n-butylphthalate (DBP), diethyl phthalate (DEP), and bis(2-ethylhexyl) phthalate (DEHP) were the most prevalent among the seven studied phthalates, with the highest concentration reached by DEHP in a bottlenose dolphin (4697.34 ± 113.45 ng/g). Phthalates esters (PAEs) concentration were higher in bottlenose dolphins (Mean ∑ PAEs: 947.56 ± 1558.34 ng/g) compared to pilot whales (Mean ∑ PAEs: 229.98 ± 158.86 ng/g). In bottlenose dolphins, DEHP was the predominant phthalate, whereas in pilot whales, DEP and DBP were more prevalent. Health markers suggested pilot whales might suffer from poorer physiological conditions than bottlenose dolphins, although high metabolic differences were seen between the two species. Phthalate levels showed no differences by ecological or biological groups, seasons, or years. This study is the first to assess the extent of plastic additive contamination in free-ranging cetaceans from a remote oceanic island system, underscoring the intricate relationship between ecological niches and contaminant exposure. Monitoring these chemicals and their potential impacts is vital to assess wild population health, inform conservation strategies, and protect critical species and habitats.