One of the most significant features of the modern countries in Africa is that an alien educational method was brought there from Europe and was combined with the indigenous African or Islamic educational structures and institutions. The new educational system, described as secular, conflicted especially with those existing systems which were religious in nature. Western education was, however, hard to resist because of all the advantages it contained in terms of preparing Africans for a new economic structure and technology, and the accompanying job opportunities. This led to the following dilemmas: Was it possible to combine the traditional and modern systems of education? Was it possible to modernise without eliminating the religious element of the educational system? These questions summarise the main problematic with which the Muslim scholars of the East African coast were confronted at the end of the nineteenth and beginning of the twentieth century’s. It was the time when the Arab Islamic civilisation provided the ideal model for Muslim practice and conduct as a new European model of life was emerging. And all this was taking place in a particular cultural context, Swahili. Some leaders of the Swahili Islamic community realized that there was no alternative to modifying their traditional system of education and opening it to the modern tendencies. One of these leaders was Sheikh al-Amin b. Ali al-Mazrui. Through his various activities, teaching and writings, he strongly influenced the educational development of Islam in East Africa. This paper presents some aspects of Islamic education in Kenya, where the traditional Islamic concept of education has encountered one of its greatest challenges: modern education. The clash between these two entirely different concepts created some problems and brought into question even fundamental elements of the previous system. Consequently, the mediaeval structure of the Quranic school was modernized and a new form, the madrasa, emerged, this also highlighted the problem of female education, so that, eventually, Muslim girls were allowed to acquire a proper education. The educational problems that arose on the East African coast at the beginning of the past century are reflected in the life activity of Sheikh al-Amin. His legacy and the clash between these two concepts had far-reaching consequences, which continue today. The particular focus of this work concerns aspects of the educational system of the East African coast at the beginning of the twentieth century. This is of great personal interest since the author has had the opportunity of working as a Catholic missionary in various Kenyan schools where he experienced the mission challenges of Islam in Kenya.