Arthrospira platensis is a cyanobacterium known for its widespread use as nutraceutical and food additive. Besides a high protein content, this microorganism is also endowed with several bioactivities related to health benefits in humans that make it a candidate for functional foods. These properties are strain and culture condition dependent. We compared, in terms of biomass productivity and protein, C-phycocyanin, and polysaccharide content, two A. platensis strains, A. platensis F&M-C256 and A. platensis F&M-C260, characterized by morphological differences. The organisms were grown in annular photobioreactors with light-emitting diodes (LED) as light source in fed-batch and semi-continuous regimes. No significant differences in biomass productivity were found between the two strains. Both strains showed a protein content >55% in all culture conditions. C-phycocyanin content was higher in A. platensis F&M-C260 in semi-continuous regime. Cellular polysaccharide (PS) content, which included intracellular polysaccharide and those bound to the cell wall, was higher in A. platensis F&M-C256 during semi-continuous cultivation. In both strains, a higher release of polysaccharide was observed at the end of the fed-batch regime. A. platensis F&M-C256 showed the advantage to form clumps which facilitate harvesting, behavior not observed in A. platensis F&M-C260 and probably related to the different predominant monosaccharide found in the PS of the two strains (i.e., rhamnose in A. platensis F&M-C256 and glucose in A. platensis F&M-C260). The results show that the two strains are suitable for commercial production of high-value products, such as protein and C-phycocyanin, while for polysaccharide production, A. platensis F&M-C256 is preferable.