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.