Malic acid in the ‘Huang guan’ pear (Pyrus pyrifolia Nakai) is the predominant organic acid associated with taste, flavor and juice quality. The effects of different treatments on malic acid-metabolizing enzymes and the related genes expression during storage have been studied. Malic acid content was higher in the peel than in the pulp. NAD-dependent malate dehydrogenase (NAD-MDH) and NADP-dependent malic enzyme (NADP-ME) correlated with gene expression during cold storage. NAD-MDH promoted malic acid synthesis, whereas NADP-ME promoted malic acid degradation. Chitosan treatment had a significantly positive effect on the activities of NAD-MDH and a negative effect on the activities of NADP-ME both in pulp and peel, and CaCl 2 just significantly affected those in peel. The gene expressions of Mdh were not significantly impacted under both treatments, in addition to the gene expression of Me under CaCl 2 treatment. An expression analysis of the proton pump gene revealed that vVAtp1 significantly negatively regulated the malic acid content, and there was a significant negative correlation between the vVpp gene and the accumulation of malic acid in the peel. Different treatments inhibited the gene expression of vVAtp2, as well as promoted gene expression of vVAtp1. Overall, both treatments attenuated enzyme activity and malic degradation of pear fruit during storage period.