Apart from being a very challenging issue, three-dimensional order in molecular thin films is of critical importance to gain and exploit a series of key properties in emerging fields like organic/hybrid photovoltaics, organic thin film transistors, sensors and plastic electronics in general. For example, the development of nanostructured bi-continuous bulk heterojunctions (BHJs) is an important advancement leading to improved photovoltaic power conversion efficiency with respect to planar heterojunctions. Here we show an original low cost, easy-to-implement and multi-tasking bottom-up approaches to modulate the supramolecular morphology in three-dimensional (3D) systems together with their optoelectronic properties, employing a “speed up and freeze” dynamic/adaptive approach. Starting from multi-planar heterojunctions (MHJs) with programmed sequence of nanoscopic layers, we induce the formation of BHJs with bicontinuous phases by the action of external stimuli. In doing this, we have employed different materials including semiconducive polymers, polymeric dielectrics and nanoparticles, investigating on the relation between the process dynamics, the material chemical properties and the desired thin-film order.