Arnica montana has been used for centuries in medicine for a variety of therapeutic purposes. The extract of the plant possesses diverse biological activities, such as anti-inflammatory, antifungal, antiviral, antitumor, tissue-regenerative, etc. The increasing market demand for arnica-containing products requires the development of an effective method for the rapid propagation of the plant, as well as the production of biomass and important pharmaceutical metabolites. Methyl jasmonate (MeJA) is an effective tool for enhancing the production of secondary metabolites in in vitro cultures. It is very useful in the synthesis of pharmaceutically significant chemicals because it mimics stress signals and activates complex metabolic pathways. For the first time, the effect of the exogenous application of MeJA on micropropagation, antioxidant capacity, and caffeoylquinic acid accumulation in arnica in vitro plantlets was evaluated. The results showed that 7-day treatment with MeJA (50, 100 and 200 μM) inhibited plant growth, modulated the activity of antioxidant enzymes, and upregulated the content of caffeoylquinic acids, total phenolics, and flavonoids. This work provides a reliable in vitro culture system for the accumulation of A. montana phenolic compounds.