Microalgae have been increasingly recognized as an alternative source of lipids, especially polyunsaturated fatty acids (PUFA) such as omega 3 and 6, being essential to carefully assess their life cycle environmental impacts. Hence, this work aims to carry out a life cycle assessment (LCA) of lipid production from the microalga Pavlova gyrans grown in different culture media and nutrient concentrations, on a “cradle-to-gate” approach. For the life cycle inventory, primary data obtained from laboratory experiments was used for the foreground processes, complemented with secondary data from LCA databases and literature for the background processes. The functional unit chosen is 1 g of lipids extracted. For the environmental impact assessment, the ReCiPe 2016 method was used, evaluating 18 midpoint indicators from an egalitarian perspective. An uncertainty estimate was performed using experimental results and the ANOVA statistical test. Results show that the organic fertilizer medium has an overall environmental impact around 1.28 to 2 times lower than the aquaculture effluent medium. Energy is the process hotspot, contributing more than 95%, on average, to the overall potential environmental impact. Alternative renewable energy scenarios were therefore evaluated. Results show that, compared to the electricity mix, renewable energies led to significant reductions in 13 environmental impact categories, such as global warming potential, which decreased by around 70 and 90% respectively for solar and wind energy, but to significant increases in 5 impact categories, such as terrestrial ecotoxicity, which increased by around 231 and 184%, and the mineral resources scarcity, which increased by around 114 and 302% respectively for solar and wind energy. The results of this study can provide valuable information to guide research and development efforts towards more sustainable processes for obtaining lipids from microalgae.