We describe a systematic study on the influence of different experimental conditions on the Kelvin probe force microscopy (KPFM) quantitative determination of the local surface potential (SP) of organic semiconducting nanostructures of perylene‐bis‐dicarboximide (PDI) self‐assembled at surfaces. We focus on the effect of the amplitude, frequency, and phase of the oscillating voltage on the absolute surface potential value of a given PDI nanostructure at a surface. Moreover, we investigate the role played by the KPFM measuring mode employed and the tip–sample distance in the surface potential mapping by lift‐mode KPFM. We define the ideal general conditions to obtain a reproducible quantitative estimation of the SP and we find that by decreasing the tip–sample distance, the area of substrate contributing to the recorded SP in a given location of the surface becomes smaller. This leads to an improvement of the lateral resolution, although a more predominant effect of polarization is observed. Thus, quantitative SP measurements of these nanostructures become less reliable and the SP signal is more unstable. We have also devised a semi‐quantitative theoretical model to simulate the KPFM image by taking into account the interplay of the different work functions of tip and nanostructure as well as the nanostructure polarizability. The good agreement between the model and experimental results demonstrates that it is possible to simulate both the change in local SP at increasing tip–sample distances and the 2D potential images obtained on PDI/highly oriented pyrolytic graphite samples. These results are important as they make it possible to gain a quantitative determination of the local surface potential of π‐conjugated nanostructures; thus, they pave the way towards the optimization of the electronic properties of electroactive nanometer‐scale architectures for organic (nano)electronic applications.