People experiencing homelessness report increased exposure to traumatic life events and higher rates of depression, anxiety, and post-traumatic stress disorder as compared with the general population. Heart rate variability-biofeedback (HRV-BF) has been shown to decrease symptoms of stress, anxiety, depression, and PTSD. However, HRV-BF has not been tested with the most vulnerable of populations, homeless adults. The purpose of this randomized controlled trial was to compare the effectiveness of an HRV-BF intervention versus a Health Promotion (HP) active control intervention focused on improving mental health symptoms among homeless adults. Guided by a community advisory board, homeless adults residing in Skid Row, Los Angeles (n = 40) were randomized to either the HRV-BF or an active HP control group and received eight weekly, 30-min sessions over two months, delivered by a nurse-led community health worker team. Dependent variables of HRV, mental health, anxiety, depression, and PTSD were measured at baseline, the 8-week session, and/or 2-month follow-up. All intervention sessions were completed by 90% (36/40) of participants. Both the HRV-BF and HP interventions showed significant increases in HRV from baseline to 2-month follow-up, with no significant difference between the intervention groups. The HRV-BF programme revealed a somewhat greater, although non-significant, improvement in anxiety, depression, and PTSD symptoms than the HP programme. The usefulness of both interventions, focused on emotional and physical health, warrants future studies to examine the value of a combined HRV-BF and HP intervention.