AbstractMicroalgae can serve as a highly productive biological feedstock for fuels and chemicals. The lipid fraction has been the primary target of research, but numerous assessments have found that valorization of co‐products is essential to achieve economic and environmental goals. The relative proportion of co‐products depends on the biomolecular composition of algae at the time of harvesting. In the present study, the productivity of lipid, starch, and protein fractions were shown through growth experiments to vary widely with species, feeding regime, and harvesting period. Four algae species were cultivated under nitrogen‐replete and ‐deplete conditions and analyzed at 3‐day intervals. Dynamic growth results were then used for life cycle assessment using the US Department of Energy's GREET model to determine optimal growth scenarios that minimize life cycle greenhouse gas (GHG) emissions, eutrophication, and cumulative energy demand (CED), while aiming for an energy return on investment (EROI) greater than unity. Per kg of biodiesel produced, C. sorokiniana in N‐replete conditions harvested at 12 days was most favorable for GHG emissions and CED, despite having a lipid content of <20%. N. oculata in N‐deplete conditions with a 12‐day harvesting period had the lowest life cycle eutrophication impacts, driven by efficient nutrient cycling and valorization of microalgal protein and anaerobic digester residue co‐products. Results indicate that growth cycle times that maximize a single fraction do not necessarily result in the most favorable environmental performance on a life cycle basis, underscoring the importance of designing biorefinery systems that ‐simultaneously optimize for lipid and non‐lipid fractions. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd