Abstract Background The relationship between a clinician and their client—the “therapeutic alliance” is a robust predictor of outcome in healthcare settings; yet, few interventions to improve alliance have been tested. Motivational interviewing is a client-centered approach that embodies many principles and strategies consistent with a strong therapeutic alliance. Purpose To examine whether alliance is enhanced by training dietitians to deliver a motivational interviewing informed health behavior change intervention (“Eating as Treatment”; EAT) as part of routine consultations with patients with head and neck cancer. The predictive ability of motivational interviewing techniques was also assessed. Methods A secondary analysis of the EAT stepped-wedge cluster-randomized controlled trial was conducted. Patients with head and neck cancer undergoing radiotherapy (n = 307) were treated by radiotherapy dietitians (n = 29) during the control (Treatment as Usual) or intervention (EAT) phase. Alliance was rated during the first and final weeks of radiotherapy, and again 4 and 12 weeks post-radiotherapy. Dietetic sessions were audiotaped. Week one sessions were objectively rated for dietitians’ use of motivational interviewing techniques. Results Generalized linear-mixed effects regressions found no effect of EAT on dietitian-rated alliance (p = .237). After excluding outliers, patient-rated alliance was 0.29 points lower after EAT training (p = .016). Post hoc analyses revealed lower patient ratings on perceived support and dietitian confidence. Hierarchical multiple regressions found that no specific motivational interviewing techniques predicted patient-rated alliance. Dietitian acknowledgment of patient challenges was related to dietitian-rated alliance (β =.15, p =.035). Conclusions Patient and dietitian ratings of alliance were high after EAT training, but not significantly improved. Further research is needed to better understand the differential impact of intervention training and delivery on patient and clinician ratings of therapeutic alliance. Clinical Trial information Trial registration number ACTRN12613000320752