Background <p><i>Lemna aequinoctialis</i> is a floating plant with potential uses as food, feed, biofuel, biomass, and pharmaceutical resources. In this study, we examined the effect of various concentrations of indole-3-propionic acid (IPA) on the growth, metabolomic, and transcriptomic profiles of <i>L. aequinoctialis</i> cultures.</p> Results <p>IPA significantly improved the growth of <i>L. aequinoctialis</i> culture and altered its metabolome and transcriptome profiles. It also increased the cellular production of aspartate, glutamate, glutamine, serotonin, tryptophan, and phytosterols. Transcriptomic analysis revealed that 7,490 genes were significantly altered by the 10 µM IPA treatment. Metabolomic and transcriptomic profiling indicated that the IPA treatment notably altered the major pathways of ‘glycerolipid metabolism’, ‘glutathione metabolism’, ‘β-alanine metabolism’, ‘alanine, aspartate, and glutamate metabolism’, and ‘starch and sucrose metabolism’. The highest productivities of serotonin, β-sitosterol, campesterol, and stigmasterol were observed on day 28 following treatment with 10 µM IPA.</p> Conclusions <p>The results of this study indicate that the application of IPA to <i>L. aequinoctialis</i> cultures significantly enhanced the growth and production of useful metabolites by affecting various metabolic pathways. This study is the first to investigate the biological effects of IPA on <i>L. aequinoctialis</i>, through an integrated analysis of metabolomics and transcriptomics. This could facilitate the large-scale cultivation of <i>L. aequinoctialis</i> for the application in various fields of agriculture and biotechnology including food, feed, and pharmaceutical industries.</p>