The role of this study was to establish the relationship between instruction cultures and student retention in Chartered Christian Universities in Kenya. The study was based on Students’ Integration Theory by Tinto (1993) and Cultural Model of Educational Management by Bush (2011). Descriptive survey research design was adopted. The targeted population was 604 year four students, 12 Academic Deans, 5 chaplains, 5 Finance Managers, and 5 Deans of students in the Chartered Christian Universities. Census method was used to sample the respondents. Interviews and questionnaires were employed in collecting data. The questionnaire was piloted and then tested for reliability using test-retest method and was validated by experts. Qualitative data was analysed and presented. Quantitative data was analysed using descriptive statistics. SPSS version 22 was applied in data analysis. Pearson Product Moment Correlations Co-Efficient and regression analysis were computed to establish relationships between the two variables. Embedded Design for mixed methods was used to integrate and present quantitative and qualitative data outcomes. It was found out that religious cultures were related to student retention (r=0.482; p=0.000) and therefore, the null hypothesis was rejected while the alternate hypotheses adopted. The study recommends that chartered Christian universities in Kenya should take advantage of their religious cultures and should find policies to strengthen the existing cultures as they develop new ones. Additionally, the Ministry of Education should develop policies that could facilitate student retention and review the existing policies on students’ retention in institutions of higher learning. Moreover, further research should be conducted.