We previously demonstrated the effectiveness of a hot water (HW) treatment (40°C for 7min) to reduce chilling injury (CI) in tomato fruit and described the global transcriptional changes associated with CI tolerance and susceptibility after 2 weeks of cold storage. In this study we describe the early transcriptional responses of HW treated and non-treated tomato fruit after a short-term cold storage (2 and 24h at 5°C). RNA-Seq analysis detected a large number of differentially expressed genes that varied from 575 (control fruit after 2h at 5°C) to 5100 (HW treated fruit after 24h at 5°C). The protective effect of HW treatment against chilling stress was related first with the up-regulation of AP2/EREBP and C2H2-type zinc finger transcription factors, which are known to induce the expression of cold-regulated genes, and second with the up-regulation of chaperonins and peptidyl-prolyl cis-trans isomerases, which prevent the denaturation and aggregation of proteins. Also, some genes related to pathogen resistance (TIR, NBS and LRR families) were up-regulated in HW treated fruit after chilling, suggesting a crosstalk between biotic and abiotic stress responses. Transcriptional changes that were induced in HW treated fruit at early stages of chilling and maintained after long-term cold storage included the up-regulation of genes related to heat stress and the down-regulation of genes related to cell wall degradation.