A five-year of monitoring (2018–2022) of the loggerhead sea turtle Caretta caretta nests in “Pozzolana di Ponente” beach on Linosa Island (Pelagie Archipelago, Italy) is here reported. To explore how temperatures affect the hatching success and the possible occurrence of any malformation in hatchlings, incubation temperature values were recorded using data loggers positioned at depths of 5 and 35 cm (for each nest) from the surface, approximately 0.5 m from the nest chamber. The obtained results highlighted important issues related to the success of hatching and the incidence of body anomalies. The temperatures recorded at different depths near the nests (5 and 35 cm) in some periods of incubation of the eggs were above optimal development temperature (i.e., ~33°C), causing high mortality rates, especially during the first two years of the survey (2018–2019). In the next three years (2020–2022), the implementation of shading cover cloths of the nests increased the survival rate and decreased the incidence of malformed individuals. Furthermore, atmospheric temperature data were extrapolated from the “Copernicus Climate Change” web service and included in our analyses to assess any changes over the timeframe analysed. Over five years (2018–2022), the average atmospheric temperature increased slightly by 1.7°C. In light of global warming, the implementation of effective and low-cost mitigation activities, such as the use of shade cloth covers to protect the nests from overheating, should be considered a suitable conservation action.