Tomato (Solanum lycopersicum) fruit is susceptible to chilling injury (CI), a physiological disorder caused by low, non-freezing temperatures that affects fruit postharvest quality. Little is known about the biochemical basis of CI, and the aim of this study was to identify proteins related to this disorder in ‘Imperial’ tomato fruit. CI and protein expression changes were analyzed during fruit ripening (0, 4, 8, and 12 days at 21 °C) after storage under chilling (5 °C) and non-chilling conditions (21 °C) for 5, 15, and 25 days. The main CI symptoms observed were uneven fruit ripening and color development, pitting, and decay. Protein analysis of two-dimensional gels showed that 6% of the detected spots (≈300) changed their expression in response to cold. The identified proteins are involved in carbon metabolism, oxidative stress, photosynthesis, and protein processing and degradation; two were related to cold stress, showing higher accumulation in non-damaged tissue of chilled fruit: thioredoxin peroxidase (TPxI) and glycine-rich RNA-binding protein (GR-RBP). This is the first report suggesting an important role for TPxI and GR-RBP in cold response during tomato fruit ripening, and they may be acting through redox sensing and regulation of gene expression at low temperature. These enzymes and the other chilling-related proteins might be working together to maintain the cellular homeostasis under cold stress conditions.