Accumulating evidence show that exercise and diet interventions are associated with improved sleep quality. Studies investigating the effects of exercise and dieting on circulating metabolomics in people with sleep disorders, particularly insomnia, are scarce. The present study is a part of a 6-month randomized lifestyle intervention on sleep disorder subjects. Seventy-two Finnish men (aged: 51.6 ± 10.1 years) with chronic insomnia symptoms who were assigned into different intervention groups completed this study (exercise n = 24, diet n = 27 and control n = 21). We found exercise and diet intervention were associated with improved sleep quality and a number of metabolites across different biochemical pathways. Although we cannot show causality, our findings may provide new insight into the biological mechanisms underlying the health effects of physical activity, diet and sleep quality. Further investigation is needed to better understand the link between lifestyle, sleep quality and metabolic health.