In this study, the influence of the laser energy on Molybdenum (Mo) and Nickel (Ni) based nanoparticles (NPs) produced by laser ablation is presented. The nanoparticles' physicochemical properties were studied for laser energy values from 70 to 300 mJ for Mo and from 100 to 250 mJ for Ni. X-ray Diffraction, Atomic Force Microscopy, Dynamic Light Scattering, Atomic Absorption, and UV–Vis Spectroscopy allowed for studying the crystalline structure, morphology, composition, and optical properties. Both samples Mo and Ni at low laser energies produce amorphous nanoparticles with sizes of 30 and 15 nm, respectively. When the laser energy increases, the crystalline structure, size, concentration, and optical properties of the molybdenum and nickel nanoparticles change. However, the shape of the nanoparticles (quasi-spherical) is independent of the laser energy. In Mo, NPs showed a monocrystalline MoO3 phase at intermediate laser energy. At high values of laser energy, Mo is the most stable structure. In Ni, NPs showed a polycrystalline NiO phase at medium laser energy. At high values of laser energy, a mixture of NiO and Ni is the most stable structure. The particle size remains constant for intermediate and high laser energy values. The main difference between the hydrodynamic diameter and the particle size was 7 nm. UV–vis spectra of Mo nanoparticles showed the formation of two compounds: (MoO4)2- and H2MoO4. UV–vis spectra of Ni nanoparticles showed that the absorbance decreased continuously above 200 nm, except for the sample prepared at 150 mJ. As the laser energy increases, the concentration of NPs increases in both cases. We concluded that the Ni sample at 150 mJ shows potential stability compared to the others due to the electrical charging of the material during the ablation process. As the most important result found in this research, it can be considered that the laser energy affects the structural, morphological, and compositional properties of Ni and Mo-based nanoparticles. Nevertheless, as expected, the most significant influence was observed in the nanoparticle concentration. The novelty of the work consists of the laser energy on the band gap and, precisely, the results for Ni-based nanoparticles. In this case, it was impossible to measure this parameter for almost all samples, possibly due to the magnetic influences, since the unoccupied d states atoms, such as Ni, are responsible for the ferromagnetism or high paramagnetism of the transition elements. There is a direct connection between the magnetic properties and the electrical conductivity. On the other hand, in the case of Mo-based nanoparticles, the influence of laser energy on the bandgap is almost negligible.