Microalgae have gained attention as alternative food sources due to their nutritional value and biological effects. This study investigated the effect of salt stress on the antioxidant activity, phenolic profile, bioa-vailability of bioactive compounds, and microbial counts in the blue-green algae Spirulina platensis and di-atom species Phaeodactylum tricornutum. Culturing these microalgae in different salt concentrations (15 35‰), we observed the highest antioxidant activity and phenolic compounds in the control groups. S. platensis (20‰) exhibited higher antioxidant activity compared to P. tricornutum (30‰), which decreased with in-creasing salt stress. Using HPLC-DAD-ESI-MS/MS, we identified and quantified 20 phenolic compounds in P. tricornutum and 24 in S. platensis. The bioavailability of these compounds was assessed through in vitro di-gestion, with the highest amounts observed in the intestinal phase. Salt stress negatively affected the syn-thesis of bioactive substances. Microbial counts ranged from 300 to 2.78x104 cfu/g for total aerobic mesophilic bacteria and from 10 to 1.35x104cfu/g for yeast/mold in P. tricornutum samples, while S. platensis samples ranged from 300 to 1.9x104cfu/g and 10 to 104 cfu/g, respectively. This study suggests that adding salt at different ratios to the nutrient media during the production of P. tricornutum and S. platensis can impact phenolic compounds, antioxidant capacity, microbial load evaluation, and in vitro bioaccessibility of the studied microalgae.