The dental erosion or decalcification of enamel is a significant clinical problem. Apple acidic beverages are thought to increase the potential for dental erosion. The purpose of this in vitro study was to investigate the effect of clove essential oil (CEO) and its active principles on tooth decalcification of apple juices. On GC-MS analysis, CEO showed a high content of eugenol (58.29%) and eugenyl acetate (19.10%). Teeth specimens were randomly divided into 5 treatment groups: control, CEO, eugenol, eugenyl-acetate, and fluoride. The specimens were exposed for 24 h and were analyzed for calcium contents using Inductively Coupled Plasma with Optical Emission Spectroscopy (ICP-OES). Data were analyzed using student t-test (P < 0.05). CEO, eugenol, and eugenyl-acetate significantly decreased the decalcification of tooth by the apple juice to only 17, 24, and 21 mgL−1, respectively. Hemolytic activity on human erythrocytes was studied to exclude the possibility of further associated cytotoxicity. It was observed that the CEO and its two lead molecules inhibit the decalcification and/or promote the remineralization caused by the apple juices. The effect of the test compounds appears to be distinct like that of fluoride treatment. CEO may, therefore, serve to be a promising adjunct to fluoride in the treatment of root caries during minimally invasive therapy.