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Spiritual well-being is very important in patients undergoing palliative care. Although psychosocial factors have been suggested to be associated with spiritual well-being, the relationship between physical signs and spiritual well-being has not been fully elucidated. The aim of this study was to explore diverse factors associated with spiritual well-being among palliative care patients in Japan. This study is a secondary analysis of a multicenter prospective cohort study involving patients admitted to palliative care units in Japan. Physicians recorded all data prospectively on a structured sheet designed for the study. The spiritual well-being score was measured using the Integrated Palliative Outcome Scale after patients’ death in regard to symptoms over the previous 3 days. We classified each patient into “better” score (0–1) and “worse” score (2–4) groups and examined diverse factors associated with spiritual well-being. Among the 1896 patients enrolled, 1313 were evaluated. In the multivariate analysis, seven variables were significantly associated with “worse” score: worse spiritual well-being on admission (2–4) (p < 0.0001), younger age (< 80) (p = 0.0001), hyperactive delirium over 3 days before death (mild/moderate/severe) (p = 0.0001), expressed wish for hastened death (yes) (p = 0.0006), worse communication among patients and families (Support Team Assessment Schedule score 2–4) (p = 0.0008), pleural effusion (present) (p = 0.037), and marital status (unmarried) (p = 0.0408). Recognizing factors associated with spiritual well-being is potentially useful for identifying high-risk groups with lower spiritual well-being at the end of life. Further study is required to investigate factors associated with patient-reported spiritual well-being.