The reconstruction of everyday diets in villages is important for understanding the diversity of diets and commerce networks of food items in premodern Japan. However, premodern diets in villages have not been well studied compared with those in cities. In this study, stable isotope analyses were performed on 23 adult human skeletons excavated from Sendaiji, a mountainous woodland village of underground Christians in Osaka in premodern Japan. No significant isotopic differences was found between individuals identified as Buddhists and those identified as Christians or between females and males. The total mean carbon, nitrogen, and sulfur isotope ratios were-21.1 ± 0.4‰, 11.6 ± 1.0‰, and 8.9 ± 1.3‰, respectively. The carbon isotope ratios in Sendaiji were the lowest among the studied premodern populations probably because these individuals consumed woodland foods that are affected by the canopy effect. No significant correlation between sulfur and nitrogen isotope ratios was apparent, suggesting that there was little contribution from marine foods or marine fertilizers to the diet of individuals in premodern Sendaiji. The relatively high nitrogen isotope ratios in Sendaiji were possibly because of the denitrification in paddy rice fields, ammonium uptake by paddy rice, use of animal fertilizers, and/ or consumption of freshwater fish. To our knowledge, this is the first detailed bioarchaeological study of the premodern diet in a mountainous village in western Japan.