We investigated the effects of increasing seawater temperature and CO2 concentration based on a high business‐as‐usual climate change scenario by year 2100 on the photosynthetic performance and productivity of Mediterranean seagrass Posidonia oceanica and alkaline phosphatase and N2‐fixing activities of microbes associated with different plant parts during winter when the plants may be thermally more vulnerable. Our results suggest that elevated CO2 and temperature benefit the overall photosynthetic performance of P. oceanica. Despite the benefits, the magnitude of respiration increased with elevated CO2 resulting in a negative carbon balance for P. oceanica in winter. This trend is contradictory to the general notion of decreased respiration in plants with increasing CO2, and warrants future investigation on the mechanisms behind the opposite trend. Changes of alkaline phosphatase activities found here may not be a direct consequence of the different treatments, but indirectly, through changes in the demand for dissolved inorganic phosphorus for N2 fixers. Of the several groups of N2 fixers tested for nifH expression (a proxy for activity of nitrogenase, the enzyme required for N2 fixation), only the unicellular N2‐fixing cyanobacterial phylotypes, UCYNB and UCYNC, actively transcribed with a positive nifH transcription response of UCYNC to elevated CO2 and temperature. Our results suggest that in future climate scenarios, the structure and diversity of N2 microbial communities associated with seagrasses may change and high‐light the importance of investigating the responses of different groups individually in their natural habitat substrates.