In aquaculture, particularly in bivalve hatcheries, the biochemical composition of algal diets has a strong influence on larval and post-larval development. Biochemical composition is known to be related to culture conditions, among which light represents a major source of variation. The effects of blue light on biochemical composition and photosynthetic rate of Isochrysis sp. (T-iso) CCAP 927/14 were assessed in chemostat at a single irradiance (300 μmol photons m−2 s−1) and compared with white light. Two different dilution (renewal) rates were also tested: 0.7 and 0.2 d−1. Relative carbohydrate content was lower under blue light than under white light at both dilution rates, whereas chlorophyll a and photosynthesis activity were higher. In contrast, carbon quota was lower and protein content higher under blue light than under white light, but only at 0.7 d−1. Despite these metabolic differences, cell productivity was not significantly affected by the spectrum. However, the nitrogen to carbon ratio and photosynthetic activity were higher at 0.7 d−1 than at 0.2 d−1, while carbon quota and carbohydrate content were lower. Our results show that blue light may influence microalgal metabolism without reducing productivity for a given growth rate, a result that should be of great interest for microalgal production in aquaculture.