Medicinal plant’s quality and safety are becoming a great interest topic worldwide, especially due to contamination with heavy metals. The main objective of this study is to determine the phytochemical composition and quantify the concentration of heavy metals, trace and macro elements in fourteen medicinal plants purchased in the Central Market of San Salvador. Samples were dried and fractionated, subsequently digested and analyzed at first by phytochemical screening and then by atomic absorption spectrometry. The concentration of twelve elements was determined, only Matricaria chamomilla exceeded the established World Health Organization limit for Cd and Cu. Acourtia nudicaulis and Turnera diffusa exceeded the permitted concentration of Ni. The concentration of these elements must be inspected in medicinal plants sold in the informal markets of El Salvador to ensure the safety and quality. To our knowledge, this is the first study of heavy metals in medicinal plants conducted in El Salvador.