Euglena gracilis is a versatile industrial microalga with remarkable metabolic plasticity in response to environmental shift. To understand the metabolic shift during growth adaptation, we present a comprehensive, multi-layered proteomics resource comparing aerobic and anaerobic growth conditions. This dataset integrates global protein abundance with site-specific phosphorylation and ubiquitination profiles, serving as a high-resolution repository for exploring metabolic transitions in E. gracilis.