Better therapeutic alliances are known to predict better treatment outcomes, but little knowledge still exists on the patient characteristics that lead to better alliances. In a sample of 128 outpatients assigned to long-term psychodynamic psychotherapy and suffering from mood and/or anxiety disorder, this study evaluated how the alliance, measured using the Working Alliance Inventory (WAI), is predicted by three different measures for assessing psychological resources and vulnerabilities: the Wechsler Adult Intelligence Scale—Revised (WAIS–R), the Defense Style Questionnaire (DSQ), and the Rorschach-based Ego Impairment Index (EII-2). All the three measures showed some ability to predict the development of the alliance during long-term therapy. The WAIS–R was found to be the strongest independent predictor, with higher intelligence scores predicting favorable development of both the patient- and therapist-rated alliance. Lower DSQ values, indicating less use of immature defenses, predicted greater improvement in the patient- but not the therapist-rated alliance. Higher EII-2 values, indicating more problematic ego functioning, predicted likewise greater patient-rated alliance improvement over the course of treatment. These findings support the value of pretreatment multimethod psychological assessment when tailoring treatment to the individual needs of patients.