Despite existing vaccines, influenza remains a significant public health burden, highlighting the need for vaccine strategies with improved safety and efficacy. Here we develop an autophagy-targeting influenza. A virus as a live attenuated vaccine by harnessing the host cell’s autophagy machinery to manipulate viral protein degradation. The virus is generated by introducing a conditionally removable autophagosome-targeting motif in the viral genome, which enables viral attenuation through autophagy-mediated degradation of the tagged viral protein in conventional cells while permitting efficient viral replication for large-scale manufacturing in engineered cell lines. The engineered virus is highly attenuated in vivo but able to induce robust humoral, mucosal, and cellular immune responses, and provides complete cross-reactive protection against homologous and heterologous viral challenges. Together, this study establishes autophagy-mediated protein degradation as a viable strategy for tuning viral attenuation, which could be adapted for the rational design of live attenuated vaccines against additional pathogens.