Marine turtles are key indicator species of ecosystem function and environmental health, however, many of their life-history features remain cryptic. Particularly, the understanding of their year-round feeding habits is critical to establish the effect of contaminants exposure through the marine food web and their adverse health consequences. Here, 24 Mediterranean loggerhead turtles (Caretta caretta) with problems related to plastic ingestion were wild-caught alive in the Tyrrhenian Sea (Central Mediterranean), their bloods and epidermis were sampled, and their carbon and nitrogen isotope ratios analyzed. Generally, δ13C values did not correlate between tissues, while δ15N values showed a linear relationship, suggesting more variability in feeding habitats than in trophic levels among turtles. For all animals, the calculated stable isotope niche was wider for skin than for blood, which support a temporal difference in feeding locations. Blood probably indicated the consumption of recent pelagic food, and skin of older more neritic prey. Bayesian mixing models were implemented for turtles sampled in Sicilian waters and results suggested that, generally, prey at low trophic levels were preferred to those at higher trophic positions. Our results support the utility of sampling blood and epidermis from alive and wild animals to investigate simultaneously newer and older ecological features of sea turtles. Further studies should aim on investigating animals in both good health and with detectable disease issues, to understand how much different threats and healthy status can influence Mediterranean loggerhead turtles’ feeding ecology.