The European clam, Ruditapes decussatus is a species with high commercial importance in Portugal and other Southern European countries. However, the development of R. decussatus culture has been limited by the highly variable patterns of natural recruitment. The development of hatchery technology will provide an alternative source of spat. The effect of six nutritional regimes on the survival, growth and biochemical composition of R. decussatus larvae were evaluated, aiming to provide crucial information on its nutritional requirements. A holistic approach incorporating all physiological response showed that the bispecific diet I. aff galbana and C. calcitrans (60/40 cell μL−1) was the more adapted throughout larval development. Moreover, the monospecific diet I. aff galbana provided an overall good performance. Larvae cannot use C. calcitrans at early stages of development; however, the inclusion of these microalgae improved late larval development. The results obtained constitute an important first step in the hatchery R. decussatus larval nutrition and a prerequisite for future work on the improvement of larval development and the optimization of feeding practices that will maximize larvae yield and minimize cost in aquaculture hatcheries.