The serum concentration and urinary excretion of flavonoids after the ingestion of guava, pineapple, and pomelo were determined using liquid chromatography-mass spectroscopy (LC-MS/MS). Each group of healthy volunteers was given 200 g of fresh fruit after overnight fasting and a 24-h flavonoid-free diet. The results demonstrate that only the glucuronic-conjugated metabolites of luteolin, quercetin, kaempferol, and myricetin were detected after fruit ingestion. The metabolites were first detected after 2 h, with the time to maximum concentration (Tmax) at 6 h. The most abundant metabolites for guava, pineapple, and pomelo were the glucuronide metabolites of quercetin (AUC0-8 5.4 ± 1.3 μg·h/mL), kaempferol (AUC0-8 9.9 ± 2.3 μg·h/mL), and luteolin (AUC0-8 6.4 ± 1.1 μg·h/mL), respectively. The flavonoids found in the 24-h urinary excretions were glucuronic- and mainly sulfate-conjugated metabolites. Quercetin metabolites were the most abundant after guava and pineapple ingestion, accounting for 900 and 700 μg, respectively. Luteolin metabolites were the most abundant after pomelo ingestion, accounting for 450 μg. The serum and urinary metabolite profiles suggested that guava and pineapple are good sources of quercetin, pineapple is a good source of kaempferol, and pomelo is a good source of luteolin. The study of flavonoid profiles may provide information for the selection of fruits as functional foods for their health benefits to help with various health conditions.