The spider crab Maja brachydactyla is an important commercial species in Europe and supports intensive fisheries in the NE Atlantic. A field survey was performed to assess long-term and consecutive interannual (2005–2010) variation of the biochemical composition of newly hatched larvae of M. brachydactyla. Larval biochemical profiles differed significantly among years, with pronounced differences being recorded in 2010. Differences among batches of newly hatched larvae were mainly explained by the contribution of triacylglycerols and, to a lesser degree, by protein and lipid content. The use of different nutrition indices is discussed. The biochemical composition of newly hatched larvae from M. brachydactyla was highly variable, even though surveyed broodstock was obtained from the same local population and was always sampled during the same season. The unpredictable biochemical profiles of newly hatched larvae may condition their survival and recruitment. This largely overlooked aspect of larval variability should be considered in future fisheries management strategies and captive production of marine organisms that still rely on wild seeds.