Nelumbo nucifera Gaertn., also known as the sacred lotus, is extensively cultivated in Southeast Asia, primarily for food and as an herbal medicine. This article reviews studies published between 1995 and 2017, on flavonoid and phenolic acid profiles and contents of 154 different cultivars of lotus. So far, some 12 phenolic acids and 89 to 90 flavonoids (47 flavonols, 25 to 26 flavons, 8 flavan-3-ols, 4 flavanons, and 5 anthocyanins) have been isolated from different parts of the lotus plant, including its leaves (whole leaf, leaf pulp, leaf vein, and leaf stalk), seeds (seedpod, epicarp, coat, kernel, and embryo), and flowers (stamen, petal, pistil, and stalk), although not all of them have been quantified. Factors affecting flavonoids and phenolic acid profiles, including types of tissues and extracting factors, are discussed in this review, in order to maximize the application of the lotus and its polyphenols in the food industry. Health promotion activities, attributed to the presence of flavonoids and phenolic acids, are described along with toxicology studies, illustrating appropriate usage and safe consumption dosages of lotus extracts. This review also presents the controversies and discusses the research gaps that limit our ability to obtain a thorough understanding of the bioactivities of lotus extracts.