Music-imaginative Pain Treatment (MIPT) is a form of music therapy addressing pain experience and affective attitudes toward pain. It includes two self-composed music pieces: one dedicated to the pain experience (pain music, PM) and the other to healing imagination (healing music, HM). Our non-experimental study addresses patients with chronic somatoform pain disorders participating in MIPT. The goal is to gain insight into the direct effect mechanisms of MIPT by combining outcome measures on both the objective physiological and subjective perception levels. The research questions are directed toward changes in pain experience and heart rate variability and their correlations. Thirty-seven hospitalized patients with chronic or somatoform pain disorders receiving MIPT participated in this study. Demographic data and psychometric measures (Symptom Check List SCL90, Childhood Trauma Questionnaire CTQ) were collected to characterize the sample. Subjective pain experience was measured by McGill Pain Questionnaire (SF-MPQ), and Heart Rate Variability by 24 h-ECG. Data analysis shows a reduction of reported pain from M = 19.1 (SD = 7.3) to M = 10.6 (SD = 8.0) in all dimensions of the SF-MPQ. HRV analyses shows a reduced absolute power during PM and HM, while a relative shift in the autonomic system toward higher vagal activity appears during HM. Significant correlations between HRV and MPQ could not be calculated. Findings are interpreted as a physiological correlate to the psychological processes of the patients. Future studies with more participants, a control-group design, and the integration of medium- and long-term effects are recommended.