The present invention disclose a process for treating a wastewater from a foodstuff factory, wherein the pipelines are cleaned and the containers are sterilized by using a water containing peracetic acid as an disinfection agent. The process of the present invention includes aerating or stirring the wastewater to decompose the peracetic acid contained therein, and carrying out an aerobic treatment to decompose the organic compounds in the wastewater. Peracetic acid is in the unstable peroxidation state, and can be decomposed into acetic acid by self-oxidation-reduction. The process of the present invention uses aeration or stirring to trigger the decomposition of the peracetic acid, so that the disinfection function thereof is reduced, and thus the aerobic treatment can be conducted to decompose the organic compounds in the wastewater.