<p>This study aimed to examine the relationships of childhood trauma and spiritual well-being with dysfunctional thoughts in individuals diagnosed with schizophrenia or bipolar disorder. This descriptive and cross-sectional study included 39 individuals diagnosed with schizophrenia and 45 individuals with bipolar disorder who were receiving treatment and care at the psychiatric clinic of a training and research hospital and at a Community Mental Health Center in a province. The research was conducted between March 15, 2023, and March 15, 2024. The data collection tools included the Sociodemographic Information Form, the Childhood Trauma Questionnaire (CTQ), the Dysfunctional Attitude Scale—Revised (DAS-R), and the Spiritual Well-Being Scale (SWBS). Childhood trauma was negatively correlated with transcendence (<i>r</i> = −&#xa0;0.217) and harmony with nature (<i>r</i> = −&#xa0;0.315) and positively correlated with anomie (<i>r</i> = 0.342). Similarly, dysfunctional thoughts were negatively associated with transcendence (<i>r</i> = −&#xa0;0.313) and harmony with nature (<i>r</i> = −&#xa0;0.326) and positively associated with anomie (<i>r</i> = 0.338) (<i>p</i> &lt; 0.05). Regression analysis showed that the dimensions of spirituality explained approximately 20% of the variance in dysfunctional thoughts, with transcendence significantly and negatively predicting dysfunctional thoughts (<i>β</i> = −&#xa0;0.34, <i>p</i> &lt; 0.05), and anomie positively predicting them (<i>β</i> = 0.30, <i>p</i> &lt; 0.05). Childhood trauma and harmony with nature did not significantly predict dysfunctional thoughts. These results indicate that while childhood trauma did not have a direct effect on dysfunctional thoughts, spiritual well-being—particularly specific dimensions such as transcendence and anomie—plays a significant role in shaping cognitive functioning.</p>