Methods for processing bonded dual alloy rotors are provided. In one embodiment, the method includes obtaining a bonded dual alloy rotor including rotor blades bonded to a hub disk. The rotor blades and hub disk are composed of different alloys. A minimum processing temperature (TDISK_PROCESS_MIN) for the hub disk and a maximum critical temperature for the rotor blades (TBLADE_MAX) is established such that TBLADE_MAX is less than TDISK_PROCESS_MIN. A differential heat treatment process is then performed during which the hub disk is heated to processing temperatures equal to or greater than TDISK_PROCESS_MIN, while at least a volumetric majority of each of the rotor blades is maintained at temperatures below TBLADE_MAX. Such a targeted differential heat treatment process enables desired metallurgical properties (e.g., precipitate hardening) to be created within the hub disk, while preserving the high temperature properties of the rotor blades and any blade coating present thereon.