This study explores the mixotrophic cultivation of using dairy byproducts, specifically scotta whey (SW), buttermilk wastewater (BMW), and dairy wastewater (DWW), to promote biomass production and enhance the composition of bioactive compounds. By assessing various concentrations (1%, 2%, and 4% v v) of these byproducts in a modified growth medium, this study aims to evaluate their effect on growth, phycocyanin (C-PC) content, and fatty acid methyl ester (FAME) profiles. The results show that the optimal biomass production was achieved with 2% scotta and dairy wastewater, reaching maximum concentrations of 3.30 g L and 3.19 g L, respectively. Mixotrophic cultivation led to increased C-PC yields, especially in buttermilk and dairy wastewater treatments, highlighting the potential for producing valuable pigments. Additionally, the FAME profiles indicated minimal changes compared to the control, with oleic and γ-linolenic acids being dominant in mixotrophic conditions. These findings support the viability of utilizing dairy byproducts for sustainable cultivation, contributing to a circular bioeconomy while producing bioactive compounds of nutritional and commercial interest.