Under environmental stress conditions, microorganisms can form a viable but non-culturable (VBNC) state, which poses a potential risk to food safety and human health. l-Malic acid (L-MA) is widely found in low-temperature fruit and vegetable juices as a common natural organic acid as well as a food additive. However, there is no report on whether L-MA in food processing can promote the formation of VBNC states. In this study, we investigated the pattern of the L-MA-induced VBNC state of Escherichia coli O157:H7 as a model organism, as well as the characteristics at the cellular and molecular levels. We discovered that L-MA can induce the VBNC state in a significant number of E. coli cells, a process accelerated by low temperatures (4 °C). Our analysis revealed that VBNC cells induced by both L-MA and 4 °C resuscitated earlier than those subjected to either condition alone, indicating increased food safety risks. For survival, L-MA-induced VBNC E. coli cells became substantially smaller and exhibited a significant decrease in respiratory activity while maintaining the basic function of the cell membrane. These cellular changes were supported by molecular-level evidence, reinforcing the implications for food safety under these conditions. This study underscores the importance of recognizing the potential risks posed by L-MA and low temperatures in food preservation, particularly in terms of underestimating the presence of harmful bacteria in food products. The insights gained from this research could contribute to the development of more effective food safety measures, particularly in the handling and processing of fruit and vegetable juices.