Autophagy is essential for early embryonic development. The acute systemic molecular response to loss of autophagic flux remains, however, unknown. Genetic ablation experiments show that loss of autophagy causes preimplantation developmental arrest in embryos, but fail to reveal the acute systemic molecular response to pharmacologically induced lysosomal failure. Here we perform a combination of pharmacological autophagy-lysosomal flux inhibition and label-free quantitative proteomics to characterize the embryonic stress response to autophagy inhibition in in vivo fertilized mouse embryos. Sustained bafilomycin A1 treatment resulted in 4- to 8-cell stage developmental arrest, while transient three hour treatment at the 1-cell stage was fully reversible, revealing a narrow resilience to acute loss of autophagic activity. Profiling the proteomic consequences of autophagy-lysosomal flux inhibition revealed extensive reprogramming of the embryonic proteome that is defined by a coordinated downregulation of ribosomal proteins and translation machinery, coupled with an enrichment of proteins associated with innate immunity and cell cycle checkpoint pathways. Together, these findings characterize an innate stress response to impairment of proteostasis that is associated with a global translational shutdown and developmental arrest. Thus, we identify autophagy as a key contributor of embryonic proteome homeostasis, and elucidate the acute stress response to its disruption that arrests development.