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The post-harvest ripening of pineapples can be effectively postponed by refrigerated storage. Nevertheless, internal browning (IB) frequently appears in pineapples after refrigerated storage during the course of the shelf life at room temperature, which is known as chilling injury (CI). In this study, the chilling injury of pineapple fruit was induced by a low temperature (6 °C) and transferred to normal-temperature storage; the best concentration of 50 μmol/L of CaCl 2 was selected by the IB appearance and electrical conductivity. Fruit quality, reactive oxygen species (ROS), antioxidants, and transcription factors were investigated. The physiological data results indicated that pineapples treated with 50 μmol/L of CaCl 2 maintained fruit quality, decreased reactive oxygen species (ROS), and enhanced the antioxidant activity of fruits, alleviating internal browning (IB) symptoms in pineapple fruit. The expressions of related genes were also consistent with the physiological changes by the transcriptome data analysis. In addition, we focused on some related metabolic pathways, including phenylpropanoid biosynthesis, MAPK pathway, plant hormone, plant-pathogen interaction, tricarboxylic acid cycle (TAC), and fatty acid biosynthesis. We performed integrative analyses of transcriptome data combined with a series of physiology and experimental analyses on the internal browning of pineapples, which will be of great significance to extending the shelf life of pineapples through molecular biology in the future.