The genus Peganum includes four species widely distributed in warm temperate to subtropical regions from the Mediterranean to Mongolia as well as certain regions in America. Among these species, Peganum harmala L., distributed from the Mediterranean region to Central Asia, has been studied and its phytochemical profile, traditional folk use, and application in pharmacological and clinical trials are well known. The review is aimed at presenting an insight into the botanical features and geographical distribution of Peganum spp. along with traditional folk uses. This manuscript also reviews the phytochemical profile of Peganum spp. and its correlation with biological activities evidenced by the in vitro and in vivo investigations. Moreover, this review gives us an understanding of the bioactive compounds from Peganum as health promoters followed by the safety and adverse effects on human health. In relation to their multipurpose therapeutic properties, various parts of this plant such as seeds, bark, and roots present bioactive compounds promoting health benefits. An updated search (until December 2020) was carried out in databases such as PubMed and ScienceDirect. Chemical studies have presented beta-carboline alkaloids as the most active constituents, with harmalol, harmaline, and harmine being the latest and most studied among these naturally occurring alkaloids. The Peganum spp. extracts have shown neuroprotective, anticancer, antimicrobial, and antiviral effects. The extracts are also found effective in improving respiratory disorders (asthma and cough conditions), dermatoses, and knee osteoarthritis. Bioactivities and health-enhancing effects of Peganum spp. make it a potential candidate for the formulation of functional foods and pharmaceutical drugs. Nevertheless, adverse effects of this plant have also been described, and therefore new bioproducts need to be studied in depth. In fact, the design of new formulations and nanoformulations to control the release of active compounds will be necessary to achieve successful pharmacological and therapeutic treatments.