Gammarid amphipods are a crucial link connecting primary producers with secondary consumers, but little is known about their nutritional ecology. Here we asked how starvation and subsequent feeding on different nutritional quality algae influences fatty acid retention, compound-specific isotopic carbon fractionation, and biosynthesis of ω-3 and ω-6 polyunsaturated fatty acids (PUFA) in the relict gammarid amphipod Pallaseopsis quadrispinosa. The fatty acid profiles of P. quadrispinosa closely matched with those of the dietary green algae after only seven days of refeeding, whereas fatty acid patterns of P. quadrispinosa were less consistent with those of the diatom diet. This was mainly due to P. quadrispinosa suffering energy limitation in the diatom treatment which initiated the metabolization of 16:1ω7 and partly 18:1ω9 for energy, but retained high levels of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) similar to those found in wild-caught organisms. Moreover, α-linolenic acid (ALA) from green algae was mainly stored and not allocated to membranes at high levels nor biosynthesized to EPA. The arachidonic acid (ARA) content in membrane was much lower than EPA and P. quadrispinosa was able to biosynthesize long-chain ω-6 PUFA from linoleic acid (LA). Our experiment revealed that diet quality has a great impact on fatty acid biosynthesis, retention and turnover in this consumer.