Catalytic deactivation caused by coking was studied in ZSM5 and zeolite Y catalysts during the isomerisation of 1-hexene under sub and supercritical conditions. The effects of varying temperature and pressure, from 220–250 °C and 10-70 bar respectively, on conversion and coke deposition were studied in both zeolites. TGA, DRIFTS, nitrogen sorption isotherms for fresh and coked catalysts and catalyst acidity measurements were compared. In ZSM5 the catalyst was stable for 96 hours. TGA and DRIFTS results show coke deposits were mainly polyolefinic and the amount decreases considerably from 18.8 wt% in the subcritical region to 10 wt% in the supercritical region. In zeolite Y, decay in conversion was observed with the rate of deactivation being slower at supercritical conditions at 235 °C and 40 bar. Naphthalene hydrogenation on NiMo/γ-Al2O3 catalyst was also studied. The effect of temperature, pressure, varying naphthalene feed concentration and operating in sub and supercritical conditions were studied. Coke deposit decreased by 38 wt% in the supercritical region. SC CO2 (Tc 31.04 °C, Pc 73.8 bar) was also used to re-activate the coked catalysts. This resulted in recovering 93% of the catalytic activity and 37% of the coke was effectively extracted by SC CO2.