The prevalence of postpartum mental illness is steadily increasing, a tendency that was exacerbated by the COVID-19 pandemic. Recent studies show that maternal depression is no longer confined to the perinatal period, and this necessitates long-term assessment and support for maternal mental health. It is critical to identify the factors that are related to depression among mothers, and this requires the development of integrated mental and physical health care encompassing both psychological aspects and intestinal microbiota, physical conditions, and dietary habits. Studies conducted in western countries have examined the association between gut microbiota and depressive disorders. However, little is known concerning postpartum mothers in healthy populations. In addition, even in healthy populations, some mothers will have severe depression. This is because mothers in Japan are typically hesitant to disclose psychiatric symptoms and tend not to consult specialists. Therefore, we conducted a cross-sectional study to investigate the association of intestinal microbiota, physical condition, and dietary habits with depressed mood in healthy mothers in Japan. We found that microbiome diversity (Shannon ) and relative abundance of butyrate-producing bacteria (e.g. , , and ), obtained using 16S rRNA gene-sequencing analysis, were associated with high levels of depressive mood. Mothers who have this attribute showed poorer sleep quality and worse physical condition than mothers with low levels of depressive mood. The evaluation of dietary habits suggested that dietary patterns high in soy products, fermented food, seaweed, and mushrooms, as well as vegetables, are beneficial for depression and intestinal microbiota (e.g. , , and ).