Metal nanoparticles (NPs) have been highlighted to improve plant growth and development in the recent years. Although positive effects of some NPs have been reported on medicinal plants, the knowledge for stimulations application of iron (Fe) and zinc (Zn) NPs is not available. Hence, the present work aimed to discover the effects of Fe NPs at 10, 20, and 30 mg L − 1 and Zn NPs at 60 and 120 mg L − 1 on growth, water content, photosynthesis pigments, phenolic content, essential oil (EO) quality, and rosmarinic acid production of lemon balm (Melissa o cinalis L.). The results showed that Fe NPs at 20 and 30 mg L − 1 and Zn NPs at 120 mg L − 1 signi cantly improved biochemical attributes. Compared with control plants, the interaction of Fe NPs at 30 mg − 1 and Zn NPs at 120 mg L − 1 led to noticeable increases in shoot weigh (72%), root weight (92%), chlorophyll (Chl) a (74%), Chl b (47%), rosmarinic acid (66%), proline (1.8fold), glycine betaine (GB, 3.3-fold), protein (3.8-fold), relative water content (8%), EO yield (3.1-fold), total phenolic content (63%), and total avonoid content (57%). The agglomerative hierarchical clustering represented three different clusters for Zn NPs levels and three clusters for Fe NPs concentrations so that NPs at 10 and 20 mg L − 1 were placed in one cluster. Heat map analysis revealed that protein, GB, EO yield, shoot weight, root weight, and proline possessed the maximum changes upon Fe NPs. Totally, the present study recommended the stimulations application of Fe NPs at 20-30 mg L − 1 and Zn NPs at 120 mg L − 1 to reach the optimum growth and secondary metabolites of lemon balm.