Silicon nanoparticles-based inks were investigated in respect of their suitability for photovoltaic and thermoelectric applications. Nanoparticles with a diameter ranging between 20 to 150 nm were functionalized in order to avoid oxidation as well as having a good stability in suspension. After inkjet-printing and drying, they were annealed up to 1000 °C under nitrogen atmosphere by both rapid thermal and microwave annealing. The influence of the annealing treatment on the structural, electrical, optical and thermal properties was investigated by Raman, SEM, electrical and optical measurements. SEM and Raman demonstrate evolution of the microstructure at temperature as low as 600 °C. Optical, electrical and thermal properties depend strongly on the annealing temperature and tend to exhibit a modification of physical properties above 800 °C when the smallest nanoparticles begin to melt. The annealing method has been identified to be of primary importance on the layer microstructure and its thermal behavior.