<jats:title>Abstract</jats:title><jats:sec><jats:title>BACKGROUND</jats:title><jats:p><jats:italic>Raphanus sativus</jats:italic> var. caudatus or Thai rat‐tailed radish (RTR) contains glucosinolates and isothiocyanates with chemopreventive effects; however, only mature plants have been investigated to date. Thus, the present study aimed to determine isothiocyanates, phenolic compounds and flavonoid compounds, antioxidant activity, cytotoxicity, and antiproliferative activity of RTR microgreens grown from seeds treated with cold plasma (21 kV for 5 min), organic elicitor (160 mmol L<jats:sup>−1</jats:sup> NaCl, 10 mmol L<jats:sup>−1</jats:sup> CaCl<jats:sub>2</jats:sub> or 176 mmol L<jats:sup>−1</jats:sup> sucrose) or both in combination. Seeds were germinated on vermiculite and sprayed with deionized water or elicitor for 7 days before harvest.</jats:p></jats:sec><jats:sec><jats:title>RESULTS</jats:title><jats:p>Cold plasma had insignificant effect on growth, whereas NaCl and CaCl<jats:sub>2</jats:sub> increased fresh weight. Plasma with CaCl<jats:sub>2</jats:sub> led to the highest total isothiocyanate (ITC) content [1.99 g kg<jats:sup>−1</jats:sup> dry weight (DW)] in RTR microgreens containing raphasatin as the only ITC detected. Plasma treatment gave the highest total phenolic content (7.56 mg gallic acid equivalents g<jats:sup>−1</jats:sup> DW), antioxidant activity from a 2,2‐diphenyl‐1‐picrylhydrazyl assay (7.70 mg trolox equivalents g<jats:sup>−1</jats:sup> DW) and ferric reducing antioxidant power assay (21.72 mg Fe<jats:sup>2+</jats:sup> g<jats:sup>−1</jats:sup> DW). Microgreen extracts from plasma showed an IC<jats:sub>50</jats:sub> value of 29.28 and 13.83 μg mL<jats:sup>−1</jats:sup> towards MCF‐7 and HepG2, respectively, with inhibitory properties on matrix metalloproteinase (MMP)‐2 and MMP‐9 proteins. Plasma enhanced <jats:italic>Bax</jats:italic> and <jats:italic>Caspase‐3</jats:italic> gene expression but reduced <jats:italic>Bcl‐2</jats:italic> and <jats:italic>MMP‐9</jats:italic> expression, indicating activation of apoptosis.</jats:p></jats:sec><jats:sec><jats:title>CONCLUSION</jats:title><jats:p>Cold plasma shows promise as an innovative tool to enhance bioactive compounds with chemopreventive benefits in microgreens. © 2020 Society of Chemical Industry</jats:p></jats:sec>