The Muslim minority in Thrace is a heterogeneous group of people regarding their cultural and linguistic identities. It consists of Muslims of Turkish origin who speak Turkish as their mother tongue, of Pomaks, who speak Pomak, and of Roma, who speak Romani. Their educational-linguistic situation is fraught with long-lasting problems, which are attributed to the inherent characteristics of 'Minority Education', a term used to describe a specific group of primary and secondary schools, situated exclusively in the area of Thrace, that operates under a special regime, as stipulated in legal instruments of international law and bilateral agreements, and can be attended only by Muslim minority children. Extensive research over the years has shown that there are serious impediments in these students learning Greek as an L2, even after the implementation of the Project for Reform in the Education of Muslim Children (PEM) and the additional educational material that targeted this particular religious minority. The results show that most of these students do not achieve a language level of A2 in Greek and, thus, exhibit low school performance. Similar results have been recorded in research papers concerning learning English as a FL, which is a compulsory school subject, by Muslim minority students in both public and minority primary schools. These students also fail to achieve the foreign language attainment level set in the school curriculum. The present paper seeks to outline the unchartered causes of this situation, delve into the language situation of Muslim students and suggest possible and viable solutions.