There are adverse effects associated with long-term opioid therapy (LTOT) for chronic pain and clinicians infrequently adhere to opioid treatment guideline recommendations for reducing risk and mitigating opioid-related harms. The primary goal of the Improving the Safety of Opioid Therapy (ISOT) intervention is to reduce harms related to prescription opioids. Secondary aims focus on enhancing the clinician-patient relationship and not having a negative impact on pain-related outcomes (to be examined through a non-inferiority analysis). The study is a cluster-randomized trial and the 44 primary care providers (PCPs) who enrolled were randomized to receive either (1) a two-hour educational workshop about a patient-centered approach to opioid therapy or (2) the educational workshop plus a collaborative care intervention delivered by a nurse care manager (NCM). Patients were assigned to the same condition as their treating PCP. ISOT was based on the chronic care model and include patient and provider activation, outcomes monitoring, and feedback to the PCP over 12 months. The NCM conducted a baseline assessment with intervention patients, tracked opioid-related behaviors and outcomes, and provided decision support to the opioid-prescribing clinician about opioid safety. Between June 2016 and October 2018, 293 veterans who were prescribed LTOT for chronic pain were enrolled, completed a baseline assessment, and assigned to a treatment condition. Participants were enrolled for 12 months. Masked assessments were conducted with participants at baseline, 6-months, and 12-months. This manuscript describes study rationale, research methods, and baseline findings.