This study investigates working alliance in blended cognitive behavioral therapy (bCBT) for depressed adults in specialized mental health care. Patients were randomly allocated to bCBT (n = 47) or face-to-face CBT (n = 45). After 10 weeks of treatment, both patients and therapists in the two groups rated the therapeutic alliance on the Working Alliance Inventory Short-Form Revised (WAI-SR; Task, Bond, Goal, and composite scores). No between-group differences were found in relation to either patient or therapist alliance ratings, which were high in both groups. In the full sample, a moderate positive association was found between patient and therapist ratings on Task (ρ = 0.41, 95% CI 0.20; 0.59), but no significant associations emerged on other components or composite scores. At 30 weeks, within-and between-group associations between alliance and changes in depression severity (QIDS, Quick Inventory of Depressive Symptomatology) were analyzed with linear mixed models. The analyses revealed an association between depression over time, patient-rated alliance, and group (p < 0.001). In face-to-face CBT, but not in bCBT, lower depression scores were associated with higher alliance ratings. The online component in bCBT may have led patients to evaluate the working alliance differently from patients receiving face-to-face CBT only.