Postharvest processing and storage not only influence the content and composition of flavonoids and phenolic acids in foodstuffs, thereby altering the amount of potentially bioavailable bioactive compounds, but can also modify their chemical form. Moreover, due to the intensive metabolism during absorption, the metabolites circulating in blood differ from the parent compounds found in food. Thus, it is difficult to predict potential in vivo effects of phenolic compounds merely by their contents in foodstuffs. Their specific bioavailability needs to be determined. This review considers studies regarding the bioavailability of flavonoids and phenolic acids from foodstuffs that meet the following criteria: providing actual concentrations of flavonoids and phenolic acids in blood plasma, body tissues, or urine, comparing differently stored or processed foods (excluding studies that use supplements or pure substances), and considering the high interindividual variability by repeated measurements in the same individuals. Only a few studies meet all of these criteria. In conclusion, processing and storage of food can have either positive or negative effects on the bioavailability of flavonoids and phenolic acids because these treatments may not only change the content, but also the chemical form of these compounds.