Cyanobacterial blooms have increased worldwide and decreases in spring blooms of diatoms in temperate aquatic ecosystems are increasingly reported. Whether such shifts in the food base positively or negatively affect primary consumer's physiological status, growth, and more broadly, ecosystem functioning, is poorly known. Here, we test how a widespread filter-feeding blue mussel from the genus Mytilus reacts to diatoms, filamenous non-toxic cyanobacteria and a mixture of the two in a 50 day feeding experiment and compare with mussels in the field. We use a multi-tracer approach to assess mussels' nutritional and physiological status. Diatoms had highest relative proportions of the essential fatty acids 20:5ω3 (EPA) and 22:6ω3 (DHA), but cyanobacteria had a high relative proportion of polyunsaturated FAs (PUFAs) especially 18:3ω3, a precursor of ω3 FAs. Bulk and amino-acid-δ¹⁵N demonstrated assimilation of cyanobacterial N or diatom N by the mussels, while fatty acid (FA) composition and δ¹³C-FA analyses demonstrated assimilation of C and FAs from diatoms. Still, C and N from both food sources were utilized when mussels were fed the mix and condition index, scope for growth (SFG; measure of energy status) and the elemental N:P ratio of mussels where higher in mussels fed cyanobacteria only, indicating better growth status in this treatment. It seems like mussels fed cyanobacteria, a food with low proportions of essential FAs compared to diatoms, were able to cover the dietary requirements through FA biosynthesis from precursor FAs. The FA composition and δ¹⁵N-results from mussels fed cyanobacteria agreed well with seasonal field measurements of mussels. Our study provides the first feeding experiment investigating how blue mussels utilize N from cyanobacteria and shows the rather positive response to this type of food. Our results suggest that imbalances in the biochemical composition of diet of consumers can be overcome through biosynthesis of essential FAs. In the context of climate change with shifting biogeochemical baselines, it is crucial to understand the biological effects of such changes in the quality of the production base.