It is well established that the transformation of abundant and cheap natural products, such as terpenoids, can produce other more valuable compounds. Thymoquinone, which has a commercial value significantly higher than that of its precursors, can be obtained by oxidation of carvacrol and thymol. In this work, a new water‐soluble MnIII PEG‐porphyrin is reported as catalyst in a water/hexane (1:1) biphasic medium for the oxidation of carvacrol and thymol into thymoquinone. The reactions were performed using tert‐butyl hydroperoxide as oxidant in the presence of ammonium acetate as co‐catalyst, reaching 94 and 78 % of conversion after 5 h of reaction for thymol and carvacrol, respectively. Experiments with oregano essential oil as substrate revealed selective transformation of thymol and carvacrol into thymoquinone. The main advantage of this biphasic system based on a water‐soluble catalyst and on substrates and products soluble in hexane, is the straightforward isolation, recovery and recycling of the catalyst by simple phase separation. Recycling studies of the MnIII PEG‐porphyrin using thymol as substrate showed high conversion values throughout four catalytic cycles.