Abstract Background Seasonal variation in microalgae production is a significant challenge to developing cost-competitive algae biofuels. Summer production can be three to five times greater than winter production, which could result in winter biomass shortages and summer surpluses at algae biorefineries. While the high water content (80%, wet basis) of harvested microalgae biomass makes drying an expensive approach to preservation, it is not an issue for ensiling. Ensiling relies on lactic acid fermentation to create anaerobic acidic conditions, which limits further microbial degradation. This study explores the feasibility of preserving microalgae biomass through wet anaerobic storage ensiling over 30 and 180 days of storage, and it presents a techno-economic analysis that considers potential cost implications. Results Harvested Scenedesmus acutus biomass untreated (anaerobic) or supplemented with 0.5% sulfuric acid underwent robust lactic acid fermentation (lactic acid content of 6–9%, dry basis) lowering the pH to 4.2. Dry matter losses after 30 days ranged from 10.8 to 15.5% depending on the strain and treatment without additional loss over the next 150 days. Long-term storage of microalgae biomass resulted in lactic acid concentrations that remained high (6%, dry basis) with a low pH (4.2–4.6). Detailed biochemical composition revealed that protein and lipid content remained unaffected by storage while carbohydrate content was reduced, with greater dry matter loss associated with greater reduction in carbohydrate content, primarily affecting glucan content. Techno-economic analysis comparing wet storage to drying and dry storage demonstrated the cost savings of this approach. The most realistic dry storage scenario assumes a contact drum dryer and aboveground carbon steel storage vessels, which translates to a minimum fuel selling price (MFSP) of $3.72/gallon gasoline equivalent (GGE), whereas the most realistic wet storage scenario, which includes belowground, covered wet storage pits translates to an MFSP of $3.40/GGE. Conclusions Microalgae biomass can be effectively preserved through wet anaerobic storage, limiting dry matter loss to below 10% over 6 months with minimal degradation of carbohydrates and preservation of lipids and proteins. Techno-economic analysis indicates that wet storage can reduce overall biomass and fuel costs compared to drying and dry storage.