Organic self-assemblies of meso-tetra (4-carboxyphenyl)porphine (TCPP) prepared in trifluoroacetic acid (TFA) and hydrochloric acid solutions at pH < 1 were studied by X-ray photoelectron spectroscopy (XPS) in order to determine the protonation state of the porphyrin building blocks present in the solid self-assembled nanostructures. XPS measurements were conducted both at room and at elevated temperatures. Room temperature N 1s spectra showed two bands with a 3:1 intensity ratio consistent with three protonated and one unprotonated nitrogen in the structures prepared in both TFA and HCl solutions. We attribute this result to TCPP existing as a 50:50 mixture of the free-base and diacid forms of the porphyrin core in the self-assembled state. Upon heating to 150 °C the TCPP/TFA and TCPP/HCl nanomaterials exhibit loss of pyrrolic hydrogens and retain different amounts of their respective counter ions. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) images of the nanostructures showed that these systems have different morphologies depending on the acid employed during fabrication and the post preparation temperature treatment. High resolution transmission electron microscopy (HRTEM) and selected area electron diffraction (SAED) of the TCPP nanostructures indicate that those prepared in HCl are crystalline while the nanoassemblies made in TFA are polycrystalline or amorphous.