Carbon capture and storage is promoted as a mitigation method counteracting the increase of atmospheric CO2 levels. However, at this stage, environmental consequences of potential CO2 leakage from sub-seabed storage sites are still largely unknown. In a 3-month-long mesocosm experiment, this study assessed the impact of elevated pCO2 levels (1,500 to 24,400?µatm) on Cerastoderma edule dominated benthic communities from the Baltic Sea. Mortality of C. edule was significantly increased in the highest treatment (24,400?µatm) and exceeded 50%. Furthermore, mortality of small size classes (0–1?cm) was significantly increased in treatment levels =6,600?µatm. First signs of external shell dissolution became visible at =1,500?µatm, holes were observed at >6,600?µatm. C. edule body condition decreased significantly at all treatment levels (1,500–24,400?µatm). Dominant meiofauna taxa remained unaffected in abundance. Densities of calcifying meiofauna taxa (i.e. Gastropoda and Ostracoda) decreased in high CO2 treatments (>6,600?µatm), while the non - calcifying Gastrotricha significantly increased in abundance at 24,400?µatm. In addition, microbial community composition was altered at the highest pCO2 level. We conclude that strong CO2 leakage can alter benthic infauna community composition at multiple trophic levels, likely due to high mortality of the dominant macrofauna species C. edule.