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The impacts of L-glutamate (L-Glu) treatment on chilling injury (CI), Ca2+ signaling, mitochondrial ultrastructure, and metabolisms of reactive oxygen species (ROS), γ-aminobutyric acid (GABA), energy of prune fruit under chilling stress were studied. The results found that the optimal concentration of L-Glu to suppress CI occurrence and maintain quality in prune fruit was 0.1 g L−1, which also enhanced the PdGLRs expression, cytoplasmic Ca2+ concentration, the contents of CaM, and CML under cold stress. Moreover, L-Glu treatment could reduce ROS accumulation and increase GABA content, and energy level, contributing to maintaining the integrity of the mitochondrial structure in cold-stored prune fruit. More importantly, PdGLRs expression and CaM/CML content positively correlated with antioxidant enzyme activities, GABA shunt, and energy status in prune fruit. These results indicated that the enhanced cold resistance of L-Glu-treated prunes might be attributed to the activated Ca2+ signaling, thus improving the antioxidant capacity, GABA, and energy levels. [Display omitted] • L-Glu could alleviate chilling injury and retain quality of cold-stored prune fruit. • L-Glu activated PdGLRs expression to induce Ca2+ signaling in prune fruit. • L-Glu maintained ROS homeostasis and the integrity of mitochondrial structure in prune fruit. • L-Glu treatment could activate GABA shunt to promote energy production in prune fruit. [ABSTRACT FROM AUTHOR]