The effects of climate change, including ocean acidification (OA), on future Southern Ocean phytoplankton community’s species composition and consequent impacts on primary production and carbon export are largely unknown. Further, changes in light availability induced by decreased vertical mixing of surface waters can lead to higher light availability enhancing potentially phytoplankton productivity in Antarctic coastal and shelf areas. Therefore, a suite of laboratory and field experiments with the two ecologically relevant Antarctic diatom species as well as a natural phytoplankton community from the Western Antarctic Peninsula were conducted under different pCO2 levels and irradiance regimes. In the two diatom species Fragilariopsis curta and Odontella weisflogii, OA did not stimulate, but inhibited growth and carbon fixation under low and medium light whereas this effect was amended under high growth irradiances. Under different dynamic light regimes, however, OA stimulated carbon fixation in the two diatoms. Yet, reduced photosynthetic efficiencies in both species indicated that this was likely a stress response to OA. In CO2-light incubation experiments with a natural community of the West Antarctic Peninsula, OA led to a decline of overall diatom abundances, including Fragilariopsis and Odontella, triggering thereby the dominance of the prymnesiophyte Phaeocystis antarctica, an inefficient vector for carbon export. In summary, these findings highlight that, under different irradiance regimes, OA is likely to induce a species shift, away from diatoms, within phytoplankton communities and to alter primary productivity of the coastal Southern Ocean with important implications for biogeochemical cycles in the future.