Spirituality is an important component of recovery for many individuals with substance use disorder (SUD). However, few studies have compared patient and physician attitudes on spirituality in SUD recovery. This study investigates patient and physician beliefs about the role of spirituality in SUD recovery and about discussing spirituality in relationship to recovery in primary care settings. Semi-structured interviews were conducted with primary care physicians recruited at two academic hospitals, and patients recruited from a faith-based residential therapeutic community. Interview transcripts were independently coded by two researchers and a grounded theory approach was used to generate themes that reflected participants' experiences. Interviews were conducted with 15 patients and 10 physicians. Patients had diverse views about the impact of spirituality on their SUD recovery, including positive, negative, and neutral. Patient and physician opinions on discussing spirituality in a primary care setting differed: most physicians felt positively towards this, believing that understanding their patients' spirituality helped them care for their patients as whole people. Many patients felt neutral, stating that they did not feel like these conversations were necessary for their care, and that they believed physicians preferred not to discuss spirituality in medical settings. Tolerance from both the patient and physician, open-ended questioning, and an individualized approach were identified as facilitators to effective discussions about spirituality and recovery. Spirituality can have diverse effects on an individual's SUD recovery. Physicians endorsed the benefits of discussing spirituality in the context of their patients' recovery, while patients expressed reservations about engaging in these conversations with their physicians. This variation in perspectives highlights the need for additional research to understand the individual and structural factors that contribute to it, as well as best practices for engaging in effective, non-judgmental conversations about spirituality in recovery.