Nanostructured silicon-based materials are good candidates for thermoelectric (TE) devices due to their low thermal conductivity, customizable electrical conductivity, and reduced cost. Generally, nanostructured TE bulk materials are obtained through compaction and sintering at high temperature (>1000 °C) of silicon nanoparticles (NPs). In order to introduce TE generators in flexible electronic devices, development of thin film TE is needed. Inkjet-printing of silicon NPs-based ink is an interesting technology for this targeted application due to its low cost and additive process. This paper presents the implementation of inkjet-printing of a silicon NPs-based ink toward the fabrication of TE material on flexible substrate and the development of a characterization method for this material. After printing, recovering of electrical properties through sintering is mandatory. Nevertheless, special care must be taken in order to keep thermal conductivity low and reduce the annealing temperature to allow the use of flexible substrates. The functional properties: electrical and thermal (measured by Raman spectroscopy), are studied as a function of the annealing process. Two types of annealing: rapid thermal annealing and microwave annealing, are investigated as well as two atmospheres: inert (N2) and reducing (N2–H2 5%).