The COVID-19 pandemic not only increased the risk of poor physical health but also brought about a crisis of spiritual health through restrictions on worship services. This study examined the spiritual health of Christians living in the era of COVID-19 and analyzed the role of personal religious practice and interpersonal trust in the church. To this end, 600 Christian adults were surveyed. This study found that women’s spiritual experience was higher than men’s and tended to be higher with older age and the length of faith. These results were linked to church duties, as duty holders had more spiritual experience than laypersons. Regarding individual religious practice and interpersonal trust, the group who frequently prayed and read the Bible and the group with high interpersonal trust in the church had high daily spiritual experiences, respectively. A comprehensive analysis through decision tree analysis showed that prayer was the variable showing the greatest difference in daily spiritual experience, while Bible reading was the second most important personal religious activity. Regarding church interpersonal trust, interaction-based trust and institution-based trust contributed to enhancing personal spiritual experience. Personal religious practice was reported as a more important variable in the promotion of spiritual experience than interpersonal factors during COVID-19.