Due to its growth under harsh acidic conditions, the microalga Galdieria sulphuraria may offer the opportunity to combine sanitation and the utilization of organic waste streams. To further deepen the knowledge of alternative waste treatment strategies that allow for holistic utilization, the control and removal of microbial contaminants via non-sterile heterotrophic G. sulphuraria on food waste hydrolysate were investigated in a continuous flow bioreactor culture. Furthermore, a substrate reservoir and harvested biomass were stored under non-sterile conditions over a period of 12 days. Despite the non-sterile conditions, the microbial load of the biomass could be kept under control. Neither the pathogen Salmonella sp. nor the coliform bacteria Escherichia coli could be found. Only nine counts per g of biomass were found for species belonging to Enterococcus spp., Enterobacteriacae, and moulds. Aerobic spore formers were counted with 2700 counts per g of biomass. Most of the aerobic mesophilic counts were formed by yeasts (1.5 × 10⁶ vs. 1.3 × 10⁶ counts per g biomass). The results revealed that, when using acidic growth conditions, contamination will not take over the culture; thus, the sterilization of waste materials can be skipped. It is assumed that such an approach can result in efficient processes for future waste-based bioeconomy strategies.