Thermally cracked naphtha represents a challenging feed for many catalytic processes. Its contaminant content and reactivity cause the deactivation of catalysts. Nevertheless, the use of an amorphous silica-alumina acid catalyst to convert and reduce the alkene content in thermally cracked naphtha was possible. The purpose of this study was to determine the cause(s) of catalyst deactivation by analysis of spent catalysts after conversion of cracked naphtha at different conditions in the range 250–350 °C, 6 MPa and WHSV of 0.5–2 h−1. It was found that nitrogen bases, suspected to be important acid catalyst poisons, were not the main cause of catalyst deactivation. Nitrogen was more abundant in deposits on the catalyst at the inlet compared to the outlet of the reactor, but the accumulated nitrogen in deposits represented only a minor fraction of the total amount of basic nitrogen to which the catalyst was exposed. Carbonaceous deposits were the main cause of catalyst deactivation and the profile of the deposition on the catalyst changed with temperature. At 325 °C the amount of deposits at the reactor outlet was higher, with lower H/C ratio and higher persistent free radical content than at the reactor inlet. Although some of the precursor species that formed deposits were present in the feed, some of the precursor species that formed deposits were produced during the conversion process. Although the contribution of acid catalysis was not ruled out, many observations in the study indicated that carbonaceous deposits formed mainly due to free radical reactions.