Microalgae produce valuable compounds in harsh environments, making them a promising resource for several industries. The traditional cultivation methods fail to achieve commercial viability, leading to decreased biomass production and high-value compound synthesis even under stressful conditions. To address these challenges, we conducted a two-stage cultivation to examine the impact of various LED lights and high salinity stress on the biomass and high-value compounds of the microalgae Chlorella sorokiniana UUIND6. When compared to the control, red light and 2-fold salinity performed best. The experimental results of the two-stage culture strategy demonstrated a substantial increase (p < 0.05) in photosynthetic pigments under red light conditions but a loss under 2-fold salinity during the second stage. Under red-light illumination, pigment concentration increased by 3.17% (chlorophyll ‘a'), 10.58% (chlorophyll ‘b'), and 62.21% for carotenoids, but was reduced by 2-fold salinity. Under 2-fold salt stress, the maximum lipid content was increased by 22.54%, followed by red LED light (15.35%). Microalgae cell size was also measured and found to be larger under red light stress (5.3 μm) and smaller under salt stress (3.3 μm). The presence of polyunsaturated fatty acids (PUFAs), monounsaturated fatty acids (MUFAs), and other molecules was verified by GC-MS and FTIR tests. Additionally, UHPLC demonstrated the considerable presence of both amino acids. The primary objective of the research was to enhance the yield of valuable compounds by improving knowledge of cultivation techniques and appropriate abiotic stressors. One such technique is the two-stage cultivation method, which enables the production of valuable compounds under diverse growth circumstances or stressors. © 2024 Elsevier Ltd