The widespread use of glyphosate as broad-spectrum herbicide has caused detrimental effects on phytoplankton communities. In the present study, the effects of glyphosate (4 mg/L) on the physiology of a resistant microalga, Chlorella sorokiniana UUIND6, were examined in both indoor and outdoor cultivation systems to correlate the findings with aquatic ecology. Notably, outdoor ponds had higher dissolved oxygen (17 mg/L) than indoor ponds, resulting in a 30% reduction in algal growth, with volumetric productivity of 0.068 g/L/D, which were 1.5-fold lower than indoor cultures. Furthermore, indoor cultures had 1.7-fold higher lipid productivity and carbohydrate productivity than outdoor cultures. To acclimatize to changing outdoor conditions, the alga modulated its cell membrane fluidity and permeability by increasing saturated fatty acids with a concomitant decrease in monosaturated fatty acids and phospholipids. The study identified C. sorokiniana as a potential candidate for outdoor cultivation for bioproduct production. Graphical abstract: (Figure presented.). © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023.