Eye movement desensitization and reprocessing (EMDR) psychotherapy can play a major role in phase-oriented treatment of complex trauma-related disorders. In terms of the theory of structural dissociation of the personality and its related psychology of action, a previous article described Phase 1 treatment—Stabilization, Symptom Reduction, and Skills Training—emphasizing the use of EMDR procedures in this phase. Phase 2 treatment mainly involves applications of EMDR processing in overcoming the phobia of traumatic memories and their subsequent integration. Phase 3 treatment focuses on further integration of the personality, which includes overcoming various phobias pertaining to adaptive functioning in daily life. This article emphasizes treatment approaches that assist therapists in incorporating EMDR protocols in Phases 2 and 3 of phase-oriented treatment without exceeding clients’ integrative capacity or window of tolerance.