The influence of ZnO seed layer thickness in Squaraine (SQ) is investigated: PC₇₁BM bulk heterojunction solar cells that incorporate ZnO nanorods. The thickness of the ZnO seed layer varies between 16–249 nm by changing the concentration of the precursor solution. With atomic force microscopy (AFM), X-Ray Diffraction (XRD), and Scanning Electron Microscopy (SEM) studies, it is shown that this approach allows to systematically tune the thickness of the ZnO seed layer without influencing seed layer grain size, or the morphology of the ZnO nanorods that are deposited on top of the seed layer. The proof-of-concept is demonstrated in SQ:PC₇₁BM solar cells. It is found that seed layers with 55 nm thickness yield the highest short circuit current densities, resulting in power conversion efficiencies of 2.5 ± 0.1%. These results are compared to SQ:PC₇₁BM solar cells prepared in planar architectures, and it is observed that both device architectures yield comparable results. The optimized nanostructured ZnO electrode enables the fabrication of BHJ devices with thick active layers without the loss in solar cell performance.