Purpose: Organic waste streams with a high microbial load have been used as nutrient sources in the cultivation of heterotrophic microalgae. However, it remains unclear whether an alga-based organic waste utilization can also result in a reduction of the microbial load, and thus in a combined waste utilization and hygenization process. Methods: The heterotrophic cultivation of the microalga Galdieria sulphuraria at a pH of 2 and 45 °C as hygenization method for digestate, which serves as nitrogen source in algae cultivation, was investigated. Attention has been paid to Salmonella sp. and spores, coming from the organic waste stream digestate and its reduction during hydrolysis and cultivation of G. sulphuraria in the resulting hydrolysate. Results: Digestate contained 0.5 × 10⁶ counts per g material, predominantly formed by aerobic, mesophilic organisms. Salmonella sp., yeast and molds, enterobacteriaceae as well as enterococci were diminished within 24 h of hydrolysis or cultivation. During hydrolysis of digestate and cultivation of G. sulphuraria the counts of aerobic, mesophilic organisms could be subsequently reduced by a log reduction factor of 3. The remaining microorganisms were almost exclusively spore forming ones which were reduced by a log reduction factor of 2 during cultivation under acidic conditions. Conclusion: It is suggested here to include the cultivation of G. sulphuraria in future waste management as hygenization process. Graphical Abstract: [Figure not available: see fulltext.]