The literature on pharmacogenomics as a tool to support antidepressant precision is burgeoning. Recently, a more active role has been argued for pharmacists in pharmacogenomic testing, with both pharmacists and family physicians perceiving pharmacist-led testing as a valuable method by which to scale this innovation for depression treatment. In this prospective, single-blind randomized controlled design, we evaluated the impact of pharmacogenomics guided versus standard antidepressant treatment of depression and anxiety, implemented in three large community pharmacies. Participants were 213 outpatients diagnosed with major depressive disorder and/ or generalized anxiety disorder, randomized to receive pharmacogenomics guided (n = 105) or standard antidepressant treatment (n = 108); participants were blinded to the study. Patient reported outcomes of depression, anxiety, disability, and treatment satisfaction were assessed at months 0, 1, 3, and 6. Hypotheses were investigated using mixed effect models on the full data. All clinical outcomes improved significantly. The primary outcome (depression) and two secondary outcomes (generalized anxiety and disability) exhibited significant time by group interactions indicating that they improved for participants who received pharmacogenomics guided treatment more so than they did for participants who received standard treatment. Treatment satisfaction improved similarly for both groups. Results contribute to a growing body of work evaluating the impact of pharmacogenomics testing to inform antidepressant medication treatment for depression and anxiety, and provides important initial evidence for the role of pharmacists in care delivery. Pharmacogenomic testing may be a valuable tool to allow pharmacists to more effectively collaborate in facilitating clinical treatment decisions. ClinicalTrials.gov registration: (NCT03591224). This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.