There is an on-going demand in recent years for safer and “greener” hair coloring agents with the global consumer awareness of the adverse effects of synthetic hair dyes. The belief in sustainability and health benefits has focused the attention of the scientific community towards natural colorants that serve to replace their synthetic toxic counterparts. This review article encompasses the historical applications of a vast array of natural plant hair dyes and summarizes the possible coloration mechanisms (direct dyeing and mordant dyeing). Current information on phytochemicals (quinones, tannins, flavonoids, indigo, curcuminoids and carotenoids) used for hair dyeing are summarized, including their botanical sources, color chemistry and biological/toxicological activities. A particular focus is given on research into new natural hair dye sources along with eco-friendly, robust and cost-effective technologies for their processing and applications, such as the synthetic biology approach for colorant production, encapsulation techniques for stabilization and the development of inorganic nanocarriers. In addition, innovative in vitro approaches for the toxicological assessments of natural hair dye cosmetics are highlighted.