Background – Although the presence of starting materials in extreme dilutions of homeopathic medicines has been established, the physico-chemical changes of these materials induced by the manufacturing steps—that is, solid–solid mixing involving grinding (trituration) and slurry mixing involving impact (succussion), followed by dilution—are still unknown. Methods – We subjected cupric oxide and zinc oxide nanoparticles (NPs) to the homeopathic processes of trituration and succussion, followed by dilution up to 6 cH. Particle image velocimetry was employed to analyze the fluid motion during succussion and its effect on the NPs. The resulting microstructural and chemical changes at different dilution steps were determined by X-ray photoelectron spectroscopy, Fourier-transform infrared spectroscopy and transmission electron microscopy. Results – The succussion triggered multi-sized bubble generation and turbulent fluid motion up to a duration of 400 ms, with maximum average velocity of 0.23 m/s. Due to 1% transfer of kinetic energy from a moving eddy with this velocity, upon collision, the rate of temperature change in a particle of size 1 µm and 1 nm was predicted to rise by approximately 102 K/s and 106 K/s respectively. During trituration, the oxide NPs reduced to metals and did not aggregate by remaining within lactose, but they converted to oxidized finer NPs after impact. Silicate chains leached from the vial cross-linked after third dilution, forming large macro-particles and encapsulating the NPs that were retained and carried at higher dilution steps. Conclusion – The results showed that the NPs sustained significant rate of temperature change due to energy transfer from moving eddies during succussion. Different physico-chemical changes, such as size reduction, successive reduction and oxidation of NPs, and morphological changes, were achieved through trituration and succussion. The retention of NPs within cross-linked poly-siloxane chains reveals the importance of both the borosilicate glass vial and the ethanol solution during preparation of homeopathic medicines.