BACKGROUNDGoat milk is considered a nutritionally superior resource, owing to its advantageous nutritional attributes. Nevertheless, it is susceptible to spoilage and the persistence of pathogens. Electron beam irradiation stands as a promising non‐thermal processing technique capable of prolonging shelf life with minimal residue and a high degree of automation.RESULTSThe effects of electron beam irradiation (2, 3, 5, and 7 kGy) on microorganisms, physicochemical properties, and protein structure and compared with conventional pasteurized goat milk (PGM). 2 kGy electron beam irradiation reduces the total microbial count of goat milk by 6‐logs, and the irradiated goat milk protein secondary structure showed a significant decrease in ɑ‐helix content. Low irradiation doses led to microaggregation and cross‐linking. In contrast, high doses (≥ 5 kGy) slightly disrupted the aggregates and decreased the particle size, disrupting the microscopic surface structure of goat milk, verified by scanning electron and confocal laser scanning microscopies.CONCLUSIONThe irradiation of goat milk with 2 kGy of electron beam irradiation of goat milk may effectively inactivate harmful microorganisms in the milk and maintain/or improve the physicochemical quality and protein structure of goat milk compared to thermal pasteurization.This article is protected by copyright. All rights reserved.