This work presents the first analytical study carried out by total-reflection X-ray fluorescence (TXRF) in the special system constituted by carbon nanoparticles impregnated with Ru and Se, which is currently being investigated as an alternative voltaic system. This study shows that conventional analytical techniques, such as atomic absorption spectroscopy (AAS) or inductively coupled plasma spectroscopy (ICPS), can produce large deviations in the metallic contents of this material, as high as 50%, due to recovery problems, mainly of Ru, in the acid leaching process. This fact can have important consequences in related research, industrial fabrication and for their environmental impact. An alternative methodology based on the quantitative direct solid analysis of metallic impregnated carbon nanoparticles by means of the TXRF technique has been developed. The suspension conditions have been optimized by the use of different programs of ultrasonic pulses, and it has been characterized by dynamic light scattering (DLS) with the aim of checking the final size distribution of the particles. This methodology has been checked for different sample size distributions of the suspension. A microscopical image and scanning electron microscopy (SEM) of the solid depositions over the TXRF sample carrier have also been performed to evaluate homogeneity from a macroscopic and microscopic point of view and, additionally, to evaluate the possible presence of matrix effects. Finally, the TXRF results were validated by means of inductively coupled plasma mass spectrometry (ICP-MS), in a direct solid way, and by elemental analysis (CHNS), which confirmed the validity of the TXRF quantitative direct solid measurements. From an analytical point of view, the more important result was the strong correlation found between the particle size distributions and the homogeneity of the depositions with respect to the uncertainty of the Ru and Se TXRF measurements, but not with respect to their nominal values. The optimum uncertainties obtained with the developed methodology were 5.9% and 2.9% for Ru and Se, respectively, for a coberture factor k = 2 (95%). Finally, the application of ICP-MS to the analysis of solid samples by suspension method has proven to be a non trivial task, at least for this nanoparticle system. The results obtained in this work indicate that the adequate modification of the fundamental ICP-MS parameters, i.e. dilution factor, RF power and nebulizer gas flow, could be the initial way to optimize the analytical results by ICP-MS.