Ordered carbon composite materials have great potential for practical applications in many areas such as energy conversion, quantum computing, biotechnologies, and electronics. In this work, we demonstrate a state-of-the-art self-assembly driven building block approach to create new layered carbon–metal composite materials with advanced properties. We fabricate molecular nanocomposites using self-assembled metal intercalated multi-layers of dithiol derivatives. The obtained structures are analysed using different characterization tools (such as X-ray photoelectron and Raman spectroscopy and atomic force microscopy) and their electronic transport properties are studied by four-point probe measurements supplemented by density functional theory calculations. This work demonstrates a new strategy for low-cost, high-yield and eco-friendly nanofabrication of hybrid organometallic membranes.