The rise in global population strains agro-industrial waste management, positioning single-cell protein (SCP) production as a cost-effective solution. Evaluating eight agro-waste residues identified wheat bran with a high solid recovery rate (67.15 %). SCP production increased from 1.29 ± 0.23 gL−1 to 21.05 ± 0.33 gL−1, achieving a microbial conversion efficiency of 90.88 % by Paradendryphiella arenariae (PG1). Nucleic acid content in SCP was reduced by 31 % using NaOH and 36 % via heat shock, significantly enhancing SCP quality, digestibility, and safety. SCP's impact on Caenorhabditis elegans (C. elegans) revealed a maximum lifespan of 18 ± 0.2 days, notable pharyngeal pumping rates (117 ± 2.541 and 67 ± 3.473 min−1 on days 5 and 10), and body bending rates (115.3 ± 0.86 and 44.8 ± 0.28 min−1 on days 5 and 10). This comprehensive approach demonstrates the promise of SCP production in sustainable waste management, resource optimization, and detailed toxicity analysis in C. elegans, broadening the potential applications of SCP in various fields.