Methoxylated flavonoids, mainly xanthomicrol and cirsimaritin that can be extracted from Dracocephalum kotschyi Boiss, have anticancer, antispasmodic and antiplatelet effects. The production of these valuable pharmaceutical compounds is one of the major goals of biotechnology studies. In this work, induced transformed roots were influenced by various concentrations of titanium dioxide nanoparticles (TiO2 NPs) at 24 or 48 h exposure time. The effects of TiO2 NPs were assessed on growth rate, activity of antioxidant enzymes, total phenol and flavonoid content (TPC and TFC) and rosmarinic acid (RA) and some flavonoids accumulation. The gene expression level of phenylalanine ammonia-lyase (pal) and rosmarinic acid synthase (ras) genes were assessed by real time PCR analysis. The transformed roots biomass was substantially increased in elicited roots in comparison with the control. The TPC, TFC and antioxidant enzymes activitywere affected by TiO2 NPs concentration and exposure time. Valuable flavonoids with anticancer characteristics along with xanthomicrol, cirsimaritin and isokaempferide exhibited an increase (70, 34.28 and 7.81-fold, respectively) versus the control. The maximum content of RA (530.5 μg g−1 FW), which was 4.30 times as great as that of control was detected in samples treated with TiO2 NPs (50 mg L−1) 24 h after elicitation. Real-time PCR analysis revealed a considerable increase in pal and ras expression rate engaged by TiO2 NPs levels and exposure time. Overall D. kotschyi transformed roots elicitation by TiO2 NPs led to a massive increment in the production of valuable anticancer flavonoids such as xanthomicrol, cirsimaritin and RA as polyphenol.