Contemporary educational institutions have been faced with emerging social-cultural, spiritual and moral issues that have brought with them new choices in views, cultural orientations, and philosophy. Ultimately, their health well-being is affected. This has created a contextual social crisis that necessitates the need to guide young people in various ways of approaching contemporary life. This article asseses the main social, moral and spiritual challenges facing students in secondary schools in Nyeri County, Kenya. The study was conducted descriptively with a total of 99 secondary school students, and 68 Christian Union(CU)/Catholic Action(CA) patrons. From the results of the study, it was established that most of the students are faced by various social, moral and spiritual challenges among others; unhealthy relationships that leads to early pregnancy among girls; religious relativism; negative influence from modern social media; and membership to pseudo-religious groups. The study, hence, recommend to various educational stakeholders on the need to change the traditional methodological approaches that have been used addressing the above mentioned challenges faced by the 21st century young generation. Hence, the need to develop a more contemporary methodoligies that can address the revolutionized social-cultural, moral and spiritual contexts. In this case, an effective complementary Christian pastoral care and counseling programmes interventions becomes vital in contemporary educational contexts.