Thin films comprising synthetically robust, scalable molecules have been shown to have major potential for thermoelectric energy harvesting. Previous studies of molecular thin-films have tended to focus on massively parallel arrays of discrete but identical conjugated molecular wires assembled as a monolayer perpendicular to the electrode surface and anchored via a covalent bond, know as self-assembled monolayers. In these studies, to optimise the thermoelectric properties of the thin-film there has been a trade-off between synthetic complexity of the molecular components and the film performance, limiting the opportunities for materials integration into practical thermoelectric devices. In this work, we demonstrate an alternative strategy for enhancing the thermoelectric performance of molecular thin-films. We have built up a series of films, of controlled thickness, where the basic units—here zinc tetraphenylporphyrin—lie parallel to the electrodes and are linked via π–π stacking. We have compared three commonly used fabrications routes and characterised the resulting films with scanning probe and computational techniques. Using a Langmuir-Blodgett fabrication technique, we successfully enhanced the thermopower perpendicular to the plane of the ZnTPP multilayer film by a factor of 10, relative to the monolayer, achieving a Seebeck coefficient of −65 μV K−1. Furthermore, the electronic transport of the system, perpendicular to the plane of the films, was observed to follow the tunnelling regime for multi-layered films, and the transport efficiency was comparable with most conjugated systems. Furthermore, scanning thermal microscopy characterisation shows a factor of 7 decrease in thermal conductance with increasing film thickness from monolayer to multilayer, indicating enhanced thermoelectric performance in a π–π stacked junction.