Antioxidants have drawn the attention of the scientific community due to being related to the prevention of various degenerative diseases. The antioxidant capacity has been extensively studied in vitro, and different methods have been used to assess its activity. However, the main issues related to studying natural antioxidants are evaluating whether these antioxidants demonstrate a key role in the biological system and assessing their bioavailability in the organism. The majority of outcomes in the literature are controversial due to a lack of method standardization and their proper application. Therefore, this study aims to compile the main issues concerning the natural antioxidant field of study, comparing the most common in vitro methods to evaluate the antioxidant activity of natural compounds, demonstrating the antioxidant activity in biological systems and the role of the main antioxidant enzymes of redox cellular signaling and explaining how the bioavailability of bioactive compounds is evaluated in animal models and human clinical trials.