Many people peel fruits, commonly persimmon, grape, apple, and peach, before eating as table fruits. Differences of bioactive compounds between peels and pulps of daily fruits are widely known but limited to individual compound because understanding of differences in their global metabolites is lack. We employed ¹H NMR-based metabolomics to explore the global metabolite differences between their peels and pulps from the fruits, which included changes of diverse metabolites in persimmon after harvest ripening. Of diverse metabolites observed among the fruits tested, various health-beneficial metabolites were present in the peels rather than the pulps and their classes were dependent on the type of fruit: gallocatechin, epicatechin and epigallocatehin only in persimmon, apple, and peach, respectively; quercetin only in persimmon and apple; kaempferol only in persimmon; chlorogenic acid only in grape and peach; neochlorogenic acid only in apple and peach; <i>p</i>-coumaric acid only in grape; phloridzin and catechin only in apple. These metabolites in the peels of each fruits were strongly correlated with free radical-scavenging activity and delay of carbohydrate digestion. Therefore, intake of whole fruits, rather than removal of their peels, were recommended for potential improvement of healthy lifespan and human wellness. This study highlights the critical role of metabolomic studies in simultaneous determinations of diverse and intrinsic metabolites in different types of fruits and thus providing a strategy for healthy eating habits of daily fruits.