The conductive polymer poly(3,4-ethylenedioxythiphene):poly(styrenesulfonate) (PEDOT:PSS) is widely used in organic electronics and printed electronics due to its excellent electronic and ionic conductivity. PEDOT:PSS films exhibit anisotropic conductivities originating from the interplay of film deposition processes and chemical structure. The previous studies found that high boiling point solvent treated PEDOT:PSS exhibits an anisotropy of 3–4 orders magnitude. Even though both the in-plane and out-of-plane conductivities are important for the device performance, the out-of-plane conductivity is rarely studied due to the complexity with the experiment procedure. Cellulose-based paper or films can also exhibit anisotropic behavior due to the combination of their intrinsic fibric structure and film formation process. We have previously developed a conductive paper based on PEDOT:PSS and cellulose which could be used as the electrodes in energy storage devices. In this work we developed a novel measurement set-up for studying the anisotropy of the charge transport in such composite materials. A tool with two parallel plates mounted with spring loaded probes was constructed enabling probing both lateral and vertical directions and resistances from in-plane and out-of-plane directions to be obtained. The measurement results were then input and analyzed with a model based on a transformation method developed by Montgomery, and thus the in-plane and out-of-plane conductivities could be detangled and derived. We also investigated how the conductivity anisotropy depends on the microstructure of the cellulose template onto which the conductive polymer self-organizes. We show that there is a relatively small difference between the in-plane and out-of-plane conductivities which is attributed to the unique 3D-structure of the composites. This new knowledge gives a better understanding of the possibilities and limitations for using the material in electronic and electrochemical devices.