Ocean acidification has been consistently evidenced to have profound and lasting impacts on marine species. Observations have shown seagrasses to be highly susceptible to future increased pCO2 conditions, but the responses of early life stages as seedlings are poorly understood. This study aimed at evaluating how projected Mediterranean Sea acidification affects the survival, morphological and biochemical development of Posidonia oceanica seedlings through a long-term field experiment along a natural low pH gradient. Future ocean conditions seem to constrain the morphological development of seedlings. However, high pCO2 exposures caused an initial increase in the degree of saturation of fatty acids in leaves and then improved the fatty acid adjustment increasing unsaturation levels in leaves (but not in seeds), suggesting a nutritional compound translocation. Results also suggested a P. oceanica structural components remodelling which may counteract the effects of ocean acidification but would not enhance seagrass seedling productivity.