SummaryAlicyclobacillus acidoterrestris is a typical endospore‐forming microorganism, whose spores are able to germinate in Not From Concentrate juice causing its spoilage. In this work, dielectric barrier discharge atmospheric cold plasma (DBD‐ACP) at the voltage of 30 kV was used to inactivate Alicyclobacillus acidoterrestris spores in NFC juice (2–8 min). The results showed spores reduced nearly 3‐log CFU mL−1 after 8 min treatment, and the morphology of spores were severely disrupted, causing the release of their contents. Furthermore, proteomic analysis showed totals of 122 and 170 different expression proteins were detected in group C (control)/Ct1 (30 kV, 4 min) and C/Ct2 (30 kV, 8 min), respectively, indicating that metabolic activities of spores including amino acid and energy metabolic, protein biosynthesis, DNA replication and spore germination are inhibited. This study confirms the inactivation of Alicyclobacillus acidoterrestris spores by DBD‐ACP and provides some new perspectives on the inactivation mechanisms of spores by DBD‐ACP.