Layer-structured 2D materials are an interesting class of compounds exhibiting strong covalent bonding within planar molecular layers and weak van der Waals interaction between them. The ability to intercalate guest species into the van der Waals gaps of 2D layered materials offers the opportunity to engineer the electronic structure of the host material for a variety of applications, such as batteries’ cathodes, photoelectrodes for H2O splitting devices or electrochromic systems. Recently, interest in intercalated 2D layered materials has grown exponentially given their potential uses as semiconducting materials with remarkable electronic and optical properties. A common example is the unique layered structure of orthorhombic molybdenum oxide (α -MoO3) which facilitates the intercalation of H2 gas molecules. Although the 2D structure enhances intercalation kinetics of different molecules and ions along the planes, in the widely reported case of 2D α-MoO3 layered films (exhibiting covalently bonded (100)-(001) planes parallel to the electrodes’ surface) such an advantage is offset by the smaller available surface area in comparison, for example, with that of nanoporous electrodes. Ideally, the most efficient system should be made of layered films formed by loosely packed nanostructures with (100)-(001) planes normal to the electrodes’ surface. This kind of morphology has been rarely reported and is acknowledged to be very difficult to fabricate through conventional synthesis methods.This contribution presents controlled synthesis and continuous optoelectronical properties tuning of layered, vertically aligned α-MoO3 structures. Samples are synthetized by means of a pulsed laser deposition system using a non-conventional ballistic approach that exploits the aerosol gas dynamic of the nanoclusters-inseminated supersonic jet flow field. Gas phase control over the kinetic energy and directionality of molybdenum oxide nucleating nanoparticles allows versatile synthesis of α-MoO3 nanostructured, hierarchically organized films. Resulting morphologies range from compact island-like films comprised of densely packed and vertically aligned layered structuresto spatially separated, vertically aligned layered structuresshowing nanowalls-like morphological features and increased specific surface area. Subsequent thermal treatment in a reactive H2-rich atmosphere allows controllable H ions intercalation and formation of HxMoO3 nanostructured semiconducting thin films where doping level, band gap energy and conductivity can be varied in a controlled fashion. Such a synthesis strategy allows for the design of a new generation of three-dimensional nanostructured electrodes combining optimized optoelectrical properties with specific morphological features that can be adapted to particular device configurations. Moreover, out-of-plane electrodes structuration discloses potential for new devices architectures beyond the common stacked flat layers approach.