The presence of N‐ and Cl‐induced superstructures is shown to drastically alter the physicochemical properties of the Cu(001) substrate. We present coherent evidence that N‐ and Cl‐c(2x2) superstructures on Cu(001) decisively impact the metalation reaction of 5,10,15,20‐tetraphenylporphyrin (2HTPP) as well as the on‐surface diffusion and assembly of this molecule. The N superstructure facilitates the metalation reaction and self‐assembled molecular domains of CuTPP are formed at room temperature (RT). In contrast, the Cl superstructure completely inhibits the self‐metalation reaction requiring metal atoms to be deposited from the top and causes 2HTPP to assemble into small clusters. A spectro‐microscopy correlation approach combining X‐ray Photoelectron Spectroscopy (XPS), Ultraviolet Photoelectron Spectroscopy (UPS), Low Energy Electron Diffraction (LEED) and Scanning Tunneling Microscopy (STM) has been utilized in this study.