Fine-scale microdot arrays of mesoporous silica were achieved by combining ink-jet printing process to Evaporation-Induced Self-Assembly (EISA) of tetraethylorthosilicate (TEOS) in the presence of triblock copolymer Pluronic F127 as surfactant. The addition of an hydrophobic organosilane, namely TFTS (CF2)5CH2CH2Si(OC2H5)3, notably improved the structural organisation of the mesoporous microdots by promoting the co-assembly of the surfactant and silica species. Moreover, by the adjustment of the ink-jet deposition parameters (i.e. drying time between two successive layers and droplet size), and by the control of the aging time of the sol before deposition, a significant structural organization between multiple successive layers inside a single microdot was observed. In addition, the study of the hydrophobicity of the arrays pointed out the influence of TFTS in combination with the surface morphology of microdots (i.e. their roughness). The contact angle followed a Cassie-Wenzel law, which revealed that a substrate totally covered by microdots could exhibit an hydrophobicity corresponding to a contact angle of 131°. As a perspective, by coupling the ink-jet printing process and EISA and by using a multinozzle system, it should be possible to generate multifunctional mesoporous microdot arrays together with a variation of the grafted function from one dot to another. Such functionalized structures could then be used as miniaturized sensors. For instance, silica microdots arrays could be functionalized with mercaptopropyl surface groups for heavy metal trapping or with precursors capable of molecular recognition for biological applications.