Plants offer a fantastic and invaluable source of natural products that can be divided in three major groups including the terpenes/terpenoids, alkaloids, and phenolic compounds. Because of their large number and great diversity, the secondary metabolites hold an immense potential in industrial and medicinal application fields. The largest chemical group is this of terpenes, encompassing up to 25,000 secondary metabolites. Some families, as Lamiaceae, Asteraceae, and Taxaceae, synthesize several terpenoid classes with a great economic value. Hairy root cultures, coming from a horizontal transfer of the wild or recombined Ri-T-DNA vector into the plant genome, have been extensively investigated to produce secondary metabolites at levels comparable to those found in the wild roots. Or, still, to reveal novel biomolecules from transgenic Ri-roots. Transformed roots exhibit a high proliferation rate, great genetic stability, and hormonal independence. Resulting in A. rhizogenes mediated transformation of plant cells, hairy roots can be harnessed for the terpenoid production on a large scale. Numerous elicitation treatments take possible to optimize the terpene accumulation in the hairy root cultures. Ri-T-DNA activation tagging and gene-silencing systems are powerful tools which can be used to reveal new function of genes involved in the pathways’ biosynthesis of terpenoids. Implementation of the CRISPR/Cas9-mediated genome editing combined to the hairy root transformation can permit to study the gene function implicated in biosynthesis pathways of secondary metabolites. Lastly, some pharmacological properties of plant terpenes/terpenoids involved in the therapy of more or less severe pathologies are reported.