Data analyzed the alteration of the host cell proteome upon the SARS-CoV-2 infection in the absence and presence of cysteine protease inhibitor, calpeptin, which is effective to virus protease Mpro and host cysteine proteases including L-cathepsin and calpain. The present data was obtained using human lung adenocarcinoma cell line Calu-3 cells (HTB-55, ATCC®) and SARS-CoV-2 strain JPN/TY/WK-521 (GISAID_ID: EPI_ISL_408667).