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<p>Lipids, in their function as trophic markers in food webs and organic matter source indicators in the water column and sediments, provide a tool for reconstructing the complexity of global change effects on aquatic ecosystems. It remains unclear how ongoing changes in multiple environmental drivers affect the production of key lipid biomarkers in marine phytoplankton. Here, we tested the responses of sterols, alkenones and fatty acids (FAs) in the diatom <i>Phaeodactylum tricornutum</i>, the cryptophyte <i>Rhodomonas</i> sp. and the haptophyte<i> Emiliania huxleyi</i> under a full-factorial combination of three temperatures (12, 18 and 24 <span class="inline-formula">^∘</span>C), three N : P supply ratios (molar ratios 10 : 1, 24 : 1 and 63 : 1) and two <span class="inline-formula"><i>p</i></span>CO<span class="inline-formula">₂</span> levels (560 and 2400 <span class="inline-formula">µ</span>atm) in semicontinuous culturing experiments. Overall, N and P deficiency had a stronger effect on per-cell contents of sterols, alkenones and FAs than warming and enhanced <span class="inline-formula"><i>p</i></span>CO<span class="inline-formula">₂</span>. Specifically, P deficiency caused an overall increase in biomarker production in most cases, while N deficiency, warming and high <span class="inline-formula"><i>p</i></span>CO<span class="inline-formula">₂</span> caused nonsystematic changes. Under future ocean scenarios, we predict an overall decrease in carbon-normalized contents of sterols and polyunsaturated fatty acids (PUFAs) in <i>E. huxleyi</i> and <i>P. tricornutum</i> and a decrease in sterols but an increase in PUFAs in <i>Rhodomonas</i> sp. Variable contents of lipid biomarkers indicate a diverse carbon allocation between marine phytoplankton species in response to changing environments. Thus, it is necessary to consider the changes in key lipids and their consequences for food-web dynamics and biogeochemical cycles, when predicting the influence of global change on marine ecosystems.</p>