The application of exogenous jasmonate can stimulate the production of ethylene, carotenoids, and aroma compounds and accelerate fruit ripening. These alterations improve fruit quality and make fruit desirable for human consumption. However, fruit over-ripening results in large losses of fruit crops. This problem is overcome by applying 1-methylcyclopropene to the fruits, due to its capacity to block the ethylene receptors, suppressing fruit ripening. In this study, treatments with only 1-methylcyclopropene and both 1-methylcyclopropene and methyl jasmonate were administered to observe whether exogenous methyl jasmonate can improve the metabolite levels in fruits with blocked ethylene receptors. Fruit pericarps were analyzed at 4, 10, and 21 days after harvest (DAH) and compared with untreated fruits. The post-harvest treatments affected primary metabolites (sugars, organic acids, amino acids, and fatty acids) and secondary metabolites (carotenoids, tocopherols, and phytosterols). However, the lipid metabolism of the tomatoes was most impacted by the exogenous jasmonate. Fatty acids, carotenoids, tocopherols, and phytosterols showed a delay in their production at 4 and 10 DAH. Conversely, at 21 DAH, these non-polar metabolites exhibited an important improvement in their accumulation.