Ewing sarcoma (EWS), a highly aggressive cancer with limited treatment options and low survival rates. Transcriptomics revealed β-Secretase 2 (BACE2) presence while BACE2 inhibition attenuated EWS cell growth, abolished tumor-initiating capacity, and altered cell cycle/metastatic signatures. To further understand the mechanism of BACE2 inhibition in EWS, we performed a global proteomic analysis of BACE2-treated vs untreated EWS cells. The proteomic dataset revealed interference at various cellular levels following BACE2 inhibition, most of which was compatible with our findings in pPDX transcriptomics and in EWS cell-based assays, including modulation of the cell cycle, metastatic signature and PI3K/Akt-related pathways.