Producing biofuel from microalgae on a large scale will require high biomass productivity using systems such as high-rate raceway ponds. The vast scale of proposed raceway ponds, spanning 247 to 988 acres per farm, suggests practices currently used in commercial monoculture agricultural systems will need to be adopted for cultivation of algae. In commercial crop production, monoculture is facilitated by a well-established seed production, distribution, and delivery system. Currently, no such system exists for microalgae. The aims of this study were to investigate the application of water-in-oil (W/O) emulsions for the storage of microalgae and the management steps required to prolong cell viability. Water-in-oil emulsions were prepared with Chlorella sorokiniana, C. minutissima, C. vulgaris var. vulgaris, and C. vulgaris to investigate the impacts of cell cultivation medium and cell acclimation prior to emulsification on cell viability during storage. For emulsions prepared with C. sorokiniana, cells that received an acclimation treatment 24 h between cell separation from the cultivation medium and emulsification survived over 100 days longer than cells that did not receive an acclimation treatment. Emulsions prepared with C. sorokiniana grown in medium containing 29.7 mM KNO3, 1.66 mM MgSO4 · 7H2O, and 0.85 mM FeSO4 · 2H2O had higher levels of viable cells after 100 days of storage compared to cells grown in medium containing 9.90 mM KNO3 and 0.20 mM MgSO4 · 7H2O with no FeSO4 · 2H2O. The results indicate that processing of cells can be managed to increase the stability of microalgae in W/O emulsions.