The heightened interest in healthy dietary practices and the preference for fresh, minimally processed foods with reduced additives have witnessed a significant surge among consumers. Within this context, bioactive compounds have garnered attention as potent agents offering beneficial biological effects when integrated into food formulations. Nevertheless, the efficacy of these bioactive compounds in product development encounters numerous challenges during various processing and storage stages due to their inherent instability. Addressing these limitations necessitates exploring novel technological approaches tailored explicitly to the application of bioactive compounds in food production. These approaches should not only focus on preserving the bioactive compounds within food matrices but also on retaining the sensory attributes (color, taste, and aroma) of the final food products. The impact of microalgae and their bioactive compounds on human health and well-being has been extensively reported in the literature. However, there is still a gap regarding the processing and stability of microalgal bioactive compounds to improve their application in the food industry. The main goal of the present work is to point out how to overcome technological challenges in enhancing the stability of bioactive compounds from microalgae for optimal food applications.