The availability of dissolved nutrients such as nitrate under extreme low temperatures is a strong determinant in the development and growth of ice diatoms. Consequently we investigated regulation of photosynthesis in a mixed culture of three diatom species, which grew in chemostats at -1 °C, 15 µmol photons m-2 s-1 under N-limitation. When nitrogen is limiting, pigment-protein complexes are one of the most affected structures under low-light conditions. The loss of integral polar thylakoid components destabilized the bilayer structure of the membrane with consequences for lipid composition and the degree of fatty acid desaturation. N-Limitation caused a decrease in monogalactosydiacylglycerol (MGDG) and a simultaneous increase in bilayer forming digalactosyldiacylglycerol (DGDG). Their ratio MGDG:DGDG decreased from 3.4±0.1 to 1.1±0.4, while 20:5 n-3 fatty acids of chloroplast related phospholipid classes such as phosphatidylglycerol (PG) increased under N-limitation. These data reveal that lipids are important components, required to sustain membrane structure under a deficiency of integral membrane bound proteins and pigments. Nonetheless, energy conversion at photosystem II is still affected by N-limitation despite this structural regulation. Photosynthetic quantum yield (Fv/Fm) and electron transport rates decreased under N-limitation caused by an increasing amount of electron acceptors (second stable electron acceptor=QB) which had slower reoxidation kinetics. The energy surplus under these conditions is stored in triacylglycerols, the main energy sink in Antarctic sea ice diatoms under N-limitation.