Phyllanthus acuminatus has been studied for its vast medical and industrial potential. Phytochemical investigations reveal that the genus is a rich source of lignans, flavonoids, phenolics, terpenoids, and other metabolites. However, the phytochemical profile elucidation of this species still needs further research. The use of eliciting compounds such as salicylic acid and methyl jasmonate has managed to increase the production of secondary metabolites in plant cell cultures. Hairy roots of Phyllanthus acuminatus were produced in 250 mL flasks with a 16 h light/8 h darkness photoperiod under diffused light with a culture time of four weeks. The elicitors salicylic acid and methyl jasmonate were tested in 50 μM and 200 μM concentrations. Non-targeted analysis was done for the different treatments using HR-MS. Identified metabolites were grouped in phenylpropanoids, phenols, and mucic acids, and statistical analysis of relative concentrations was achieved. A significant change in phenols’ relative concentrations appeared in the elicitations with salicylic acid. Because of the elicitation treatment, specific compounds increased their concentrations, some of which have known pharmacological effects and are used in treating chronic diseases. The best elicitation treatment was salicylic acid 50 μM as it increased by more than 100% the general content of phenols and phenylpropanoid derivates and triplicates the concentration of mucic acid derivates in treated hairy root extracts. The application of non-targeted analysis showed interesting changes in phytochemical concentration due to elicitation in Phyllanthus acuminatus hairy roots.