Carbazole-based self-assembled monolayers (PACz-SAMs), anchored via their phosphonic acid group on a transparent conductive oxide (TCO) have demonstrated excellent performance as hole-selective layers in inverted perovskite solar cells. However, the influence of the TCO microstructure on the effective work function (WF) shift after SAM anchoring and WF variations at the micro/nanoscale have not been extensively studied yet. Herein, we used Kelvin probe force microscopy (KPFM), electron backscatter diffraction (EBSD) and ultraviolet photoelectron spectroscopy (UPS) to investigate the effect of microstructure of Sn-doped In2O3 (ITO) on the WF distribution upon 2PACz-SAMs and NiOx/2PACz-SAMs application. For this, ITO substrates with amorphous and polycrystalline (with nanoscale and microscale-sized grains) microstructures are studied. A correlation between the ITO crystal grain orientation and 2PACz-SAMs local potential distribution was found via KPFM and EBSD. These variations vanish for amorphous ITO or when adding an amorphous NiOx buffer layer, where a uniform and homogeneous surface potential distribution is mapped. UPS confirmed the overall ITO WF increase after 2PACz-SAMs deposition. Considering the importance of polycrystalline TCOs as high mobility and broadband transparent electrodes, we provide insights to ensure uniform WF distribution and enhance the performance of hole transport SAMs in perovskite solar cells.