During post-harvest storage, vitamins and health promoting compounds of fresh fruits are prone to change. Variation in ascorbic acid (ASC), total vitamin C (VitC), total phenolic (TPC) and total flavonoid (TFC) and antioxidant capacities (ACs) were studied during storage of fresh fruits (31 species) for 14 days at three different temperatures. During storage, ASC (1.6–90.0%) and VitC (0.1–71.6%) contents decreased significantly in most of the fruits, irrespective to the storage temperature. Interestingly accumulation of ASC (1.0–245.0%) and VitC (0.5–102.8%) was also observed in some fruit species; Musa paradisiaca, Aegal marmelos, Citrus aurantifolia and Passiflora edulis. All the fruits with the highest rate of accumulation of ASC and VitC are climacteric fruits; Musa paradisiaca, Persea americana etc. In Psidium guajava, almost all the measured health promoting compounds were significantly lost during storage. In most of the under-utilized fruits, significant loss in TPC (Artocarpus heterophyllus (‘Wela’) at room temperature: 87.4%), TFC (Averrhoa carambola: 100.0%) and ACs could be observed. The highest percentage of losses (100.0%) in DPPH radical scavenging assay and Ferric reducing antioxidant potential were observed in Citrullus lantanus. According to the results of multivariate analysis of variance (MANOVA), there is a statistically significant effect (p < 0.0005) of fruit species, storage temperature and an interaction effect of those on changing rates of measured antioxidants. The reduction rates of measured antioxidants are significantly highest at room temperature, while which are significantly highest under freezing conditions compared to refrigeration. Refrigeration temperature is recommended for optimization of preservation of vitamin C and antioxidants during storage of fresh fruits.