Addiction continues to be a major public health concern, and rates of relapse following currently-available treatments remain high. There is increasing interest in the adjunctive use of mindfulness-based interventions, such as yoga, to improve treatment outcomes. The current study was a preliminary naturalistic investigation of a novel trauma-informed yoga intervention in an inpatient treatment program for women with substance use disorder (SUD). Changes and differences in somatic symptoms, psychiatric symptoms, and psychological mechanisms were evaluated in women receiving treatment-as-usual (n = 36) and treatment-as-usual plus the yoga intervention (n = 42). For both groups, statistically significant within-subjects changes were present for somatic and psychiatric symptoms, cravings, self-efficacy, and multiple facets of impulsivity and mindfulness. Compared to standard treatment alone, participants in the treatment plus yoga condition significantly improved in range of motion and the Lack of Premeditation facet of impulsivity. Although most domains were not selectively affected, these initial within-treatment findings in this naturalistic evaluation suggest some promise for adjunctive yoga and a need for further evaluation, especially using larger samples and longer term follow-up.