Norharmane is an indole alkaloid that can be found in several terrestrial plants, as well as in some dinoflagellates and cyanobacteria. The aim of this study was to focus on the way this metabolite impacts the plant metabolism of the model species Arabidopsis thaliana. This metabolite caused increase of secondary and adventitious roots, as well as torsion, toxic effects, and a decrease in root length. Moreover, norharmane altered the cellular arrangement, resulting in unfinished cell walls, decreased auxin content and inhibited PIN proteins activity. All the alterations suggest that norharmane alters polar auxin transport by inhibiting PIN2, PIN3 and PIN7 transport proteins, thus causing a significant inhibitory effect on the growth of A. thaliana seedlings.