Euglena gracilis is a source of high-value natural products. A major factor affecting consistent production of Euglena biomass is strain stability. Cryopreservation is a leading strategy for cell-line storage that helps ensure process reproducibility. We developed a simple cryopreservation protocol for heterotrophically cultured Euglena that enables the recovery of cells after 1 year with a cell viability of ≅80%. This protocol is suitable for labs interested in the long-term preservation of heterotrophic cultures of Euglena and related species.