Stress negatively affects physical and mental health, leading to conditions like depression and anxiety. Diet and gut microbiota are crucial factors influencing stress and mental health. We hypothesized that not a single nutrient but a combination of nutrients affects stress response via gut microbiota. This study investigated the relationships among diet quality, gut microbiota, and stress in healthy adults, specifically examining the associations between Nutrient Rich Food index 9.3 (NRF9.3) scores, gut microbiota, and stress responses. Data were collected from the "Sukoyaka Health Survey," which included the Food Frequency Questionnaire (FFQ), Brief Job Stress Questionnaire (BJSQ), and gut microbiota analysis of 1058 participants. Stress scores were calculated using the BJSQ, and diet quality was assessed using the NRF9.3. Cluster analysis was used to create clusters based on stress scores, and diet and gut microbiota were compared between clusters. A probabilistic network modeling was used to evaluate the relationships among diet, gut microbiota, and stress. Participants with higher stress scores had lower NRF9.3 scores and altered gut microbiota, particularly a lower abundance of Lachnospira. Foods like natto, tomatoes, and green peppers were consumed less by the high-stress group. Using exploratory probabilistic network modeling, our analysis predicted that higher consumption of these foods was associated with an increase in the NRF9.3 score and may reduce stress by enhancing Lachnospira abundance. These findings suggest that the consumption of natto, tomatoes, and green peppers may contribute to increasing NRF9.3 scores and the abundance of Lachnospira, and potentially decreasing the physical and mental stress response scores.