Juncus species are valuable sources of phenanthrene compounds that have been used in traditional Chinese medicine for thousands of years. Effusol and juncusol are the most investigated compounds reported to have antimicrobial and anticancer effects; however, to date, their effects on higher plants have not been investigated. In this study, we examined the effects of effusol and juncusol on the growth and other biochemical parameters of the dicot model plant Arabidopsis thaliana in a concentration-dependent manner with a focus on polyamine metabolism. Phenanthrene induced toxic effects on plant growth and development, while effusol and juncusol induced higher biomass and maintained antioxidant defence mechanisms associated with reduced polyamine degradation. Taken together, our results suggest that these compounds could be good candidates for new biopesticide or biostimulant plant growth regulators in the future.