This study determined growth and lipid accumulation in Nannochloropsis sp. MASCC 11 cultivated at different pH, temperatures, and CO 2 concentrations in 10-day period. The suitability for biodiesel production was also evaluated based on the fatty acid profiles of microalgae lipid. Nannochloropsis sp. MASCC 11 showed an excellent tolerance to acidic pH (as low as 4.0), high temperatures (at least 40°C), and high CO 2 concentrations (5%–15%), which are major stressed conditions in flue gas. The highest algal biomass was acquired at pH of 9.0 (0.44 g L −1), a temperature of 35°C (0.63 g L −1), and a CO 2 concentration of 5% (2.27 g L −1). Maximum lipid production was obtained at pH of 6.0 (108.2 mg L −1), a temperature of 35°C (134.6 mg L −1), and a CO 2 concentration of 5% (782.7 mg L −1). Synthesis of polyunsaturated fatty acids (PUFAs) in biomass was stimulated under high CO 2 concentrations, remaining above 80% of total fatty acids, mainly composed of C16:3, C18:2, and C18:3. This led to the algae-based biodiesel having a lower oxidation stability, better cold flow properties, and other parameters such as its kinematic viscosity, cetane number, and specific gravity complied with ASTM or EN 14214 biodiesel specifications. Therefore, the improvement of oxidative stability needs to be considered before Nannochloropsis sp. MASCC 11 lipid can be used for biodiesel production, even if this species can grow well under stressful conditions.