Despite growing concern about the occurrence of microplastics in aquatic ecosystems there is only rudimentary understanding of the pathways through which any adverse effects might occur. Here, we assess the effects of polystyrene microplastics (PS-MPs; <70 µm) on a common and widespread algal species, Chlorella sorokiniana. We used laboratory exposure to test the hypothesis that lipids and fatty acids (FAs) are important molecules in the response reactions of algae to this pollutant. Cultivation with PS-MPs systematically reduced the concentration of essential linoleic acid (ALA, C18:3n-3) in C. sorokiniana, concomitantly increasing oleic acid (C18:1n-9). Among the storage triacylglycerols, palmitoleic and oleic acids increased at the expenses of two essential fatty acids, linoleic (LIN, C18:2n-6) and ALA, while PS-MPs had even Final submitted version: March 09 2020 more pronounced effects on the fatty acid and hydrocarbon composition of waxes and steryl esters. The FA composition of two major chloroplast galactolipids, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), were affected implying changes in the conformational structure of photosynthetic complexes that can impair the photosynthesis. These data reveal how exposure to polystyrene microplastics can modify the concentrations of lipid molecules that are important intrinsically in cell membranes, and hence the lipid bilayers that could form an important barrier between algal cellular compartments and plastics in the aquatic environment. Changes in lipid synthesis and fatty acid composition in algae could also have repercussions for food quality, growth and stressor resistance in primary consumers. We advocate further studies of microplastics effects on the lipid composition of primary producers, and of their potential propagation through aquatic food webs.Main finding: Polystyrene causes fundamental changes in lipid composition of widespread algae opening a new front in understanding microplastic effects on food webs.