Structural, optical and electrical properties of Al+MoO3 and Au+MoO3 thin films prepared by simultaneous magnetron sputtering deposition were investigated. The influence of MoO3 sputtering power on the Al and Au nanoparticle formation and spatial distribution was explored. We demonstrated the formation of spatially arranged Au nanoparticles in the MoO3 matrix, while Al incorporates in the MoO3 matrix without nanoparticle formation. The dependence of the Au nanoparticle size and arrangement on the MoO3 sputtering power was established. The Al-based films show a decrease of overall absorption with an Al content increase, while the Au-based films have the opposite trend. The transport properties of the investigated films also are completely different. The resistivity of the Al-based films increases with the Al content, while it decreases with the Au content increase. The reason is a different transport mechanism that occurs in the films due to their different structural properties. The choice of the incorporated material (Al or Au) and its volume percentage in the MoO3 matrix enables the design of materials with desirable optical and electrical characteristics for a variety of applications.