The prevalence of postpartum mental illness is steadily increasing, exacerbated particularly by the COVID-19 pandemic. Recent studies indicate that maternal depression is no longer confined to the perinatal period, necessitating long-term assessment, and support for maternal mental health. Identifying risk factors for mothers’ depression is thus critical and requires development of integrated mental and physical health care that encompasses not only psychological aspects but also gut microbiota, physical condition, and eating habits. Western countries have examined the association between gut microbiota and depression in clinical samples. However, studies focusing on postpartum mothers are still limited, and moreover, no large-scale studies have yet been conducted with nonclinical participants. To address this gap, we investigated gut microbiota, physical condition, and dietary habits associated with risk of depression in nonclinical Japanese mothers. We found that microbiota diversity (Shannon α) and relative abundance of butyrate-producing bacteria (e.g., Lachnospira, Faecalibacterium, Lachnoclostridium) with 16S rRNA gene-sequencing analysis were associated with high risk of depression. Furthermore, even among nonclinical mothers, high-risk mothers showed poorer sleep quality, worse physical condition, and lower consumption of staple foods, milk, cheese, yogurt, and lactobacillus beverages compared to low-risk (healthy) mothers. Evaluation of dietary habits using the Japanese Dietary Index (JDI) suggested that consumption of a Japanese-style diet is beneficial to physical and mental health, including intestinal microbiota (e.g., Agathobacter, Subdoligranulum).