The evolution of sheet resistance Rs of n-type and p-type conductive AlxGa1–xAs layers (x = 0.3, 0.6, and 1.0) during proton irradiation was investigated. The threshold dose Dth to convert a conductive layer to a highly resistive one is slightly different for n- and p-type samples with similar initial free carrier concentration and does not depend on the Al content. The thermal stability of the isolation, i.e., the temperature range for which the Rs is maintained at 109 /sq, was found to be dependent on the ratio of the carrier trap concentration to the original carrier concentration. The thermal stability of isolated p-type samples is limited to temperatures lower than 450 °C. The temperature of 600 °C is the upper limit for the n-type samples thermal stability.