It is inevitable that in a multi-religious community, there are conflicts often happening between people with different religions. Therefore, it is a need to identify the learning material to establish undesrtanding through interfaith activities. Thre reserach was conducted in State Senior High School 9 of Manado, North Sulawesi, Indonesia. This paper shows that school environment that is conducive for embedding values of religious tolerance. The realization of collaboration among the school community leads to the better tolerant life. These activities, non-Muslim students are participating and respecting each other. Muslim students are given times and direction for doing prayers such as dhuha as sunnah prayer and dhuhur and ashar as obligatory prayers. In fact, the result shows that that there has no conflict occurred which is caused by intolerance. Moreover, inhibiting factors of embedding process of values of religious tolerance in Islamic education in Public Senior High School 9 of Manado are, among others, levels of students' capability and emotional maturity which are not similar, the lack of teachers of Islamic, Catholic, Hindu and Buddhist educations, as well as the place for learning Islamic lesson is still functioned as musholla.