This qualitative study sought to identify the critical aspects that need to be addressed in eleven indigenous primary schools participating in the full-time schools´ federal program in the state of Baja California, Mexico. This has been done by using a case study design, interviewing individually each principal, and the schools´ supervisor. The program operates in Mexico since 2007, and assigns direct financial resources to schools, but changes the teachers´ workload by increasing the number of working hours (from 12:30 to 15:00) and by introducing the use of teaching strategies intended to strengthen their syllabus, including language and mathematics. The ultimate purpose is that students achieve the learning outcomes required by the official curriculum. The findings show that the principals acknowledged a malfunction of the program, due mainly to the local authorities’ failure to follow the operation handbooks, for example, delaying the delivery of financial resources. Also, they reported having heavier administrative demands since they must comply with all the educational system´s requirements as well as with the full-time schools´ federal program. Despite these difficulties, the principals considered that there have been improvements in their schools and benefits for their pupils, noticeable mainly in the construction of classrooms, acquisition of equipment and educational resources, but above all, for the school-based provision of food. Undoubtedly, participating in the program has benefited the indigenous schools, most of them located in marginalized areas, but the children's low educational performance has not been reverted and they still lag behind their peers from regular primary schools.