PURPOSE: Studying the role of nanoparticles in plant cryopreservation is essential for developing innovative methods to conserve plant genetic resources amid environmental challenges. This research investigated the effects of gold (AuNPs), silver (AgNPs), and zinc oxide (ZnONPs) nanoparticles on the structural integrity, genetic stability, and metabolic activity of cryopreserved plant materials with medicinal properties. METHODS: Shoot tips from two bleeding heart ( RESULTS: Electron microscopy observations of LN-derived plant material confirmed the production of micro-morpho-structurally stable cells. It was found that nanoparticles could penetrate the cell and accumulate in its various compartments, including the nucleus. As for the genetic analysis, SCoT markers identified polymorphisms in 11.5% of 'Gold Heart' plants, while RAPDs detected mutations in 1.9% of 'Valentine' specimens. Analysis of Molecular Variance (AMOVA) indicated that in the 'Valentine' cultivar, all genetic variation detected was within populations and not significantly affected by nanoparticle treatments. In 'Gold Heart', the majority (94%) of genetic variation detected was within populations, while 6% was attributed to nanoparticle treatments (mostly the application of 15 ppm ZnONPs). The application of nanoparticles significantly influenced the metabolic profile of bleeding heart plants, particularly affecting the synthesis of phenolic acids and aldehydes, as well as the antioxidant mechanisms in both 'Gold Heart' and 'Valentine' cultivars. The content of proteins was altered in 'Gold Heart' plants but not in 'Valentine'. CONCLUSION: The results suggest that different types and concentrations of NPs have varying effects on the production of specific metabolites, which could be harnessed to modulate plant secondary metabolism for desired pharmacological outcomes.