The hatching success of nests deposited by olive ridley turtles Lepidochelys olivacea during aggregated nesting events (‘arribada’) is typically low and the underlying mechanisms are not clear. In this study, temperature, oxygen and carbon dioxide partial pressures (PO2 and PCO2) of in situ nests as well as nests relocated into a hatchery with clean sand were monitored throughout incubation. Hatching success of hatchery nests was significantly higher than in situ nests (83.1 vs. 21.6%) and mainly resulted from higher mortality of early-stage embryos. During the first half of incubation, temperature and PCO2 were higher (by 0.6°C and 0.7 kPa, respectively) and PO2 was lower (by 1.1 kPa) within in situ relative to hatchery nests. Because embryo metabolism does not interfere significantly with nest gas contents during the first half of incubation, these results suggest that the greater content of organic matter and/or microorganisms in the sand surrounding in situ nests had an effect on nest gas contents. As PO2 and PCO2 differences were relatively small, microbial activity (such as fungal and bacterial infection) may have caused the early embryo mortality found in situ. Moreover, our results suggest that during the second half of incubation, neither PO2 nor PCO2 reached threshold levels that resulted in the death of embryos or hatchlings. Overall, this study showed a clear benefit of using clean sand to increase hatchling production in arribada beaches and highlights the importance of further investigating the relationship between nest micro-environment, sand microbial activity and embryo development under natural conditions during these unique nesting events.