Harvested tomatoes were stored under atmospheres that were normoxic, anoxic, or modified (altered O₂ and CO₂ concentrations). Each atmosphere was created by storing the tomatoes at 25°C for up to 8 days in different kinds of pouches. During storage, metabolites of the tomatoes were measured using metabolomics. We obtained score plots of the metabolites on eighth day of storage by principal component analysis. There was a tendency for groups to be divided on the basis of score plot according to the composition of each gas. PC1 and PC2 seemed to correspond to the influence of O₂ and CO₂ concentrations, respectively, and the total contribution rate of the two axes was 72%, so that we concluded that the metabolites were affected mainly by O₂ and CO₂ concentrations. The results indicate that metabolomics may be an effective tool to reveal the relationship between metabolic state of harvested fruits and the atmosphere.