The modern paradigm of education development has new demands on the professional and personal traits of a teacher, in particular, the ability to organize research activity of schoolchildren and to support their interest in science. The research competence of future teachers is a key characteristic that provides these skills. Properly organized research activity of future science teachers contributes not only to their research competence development, but also to their self-confidence as a professional, and thus, supports their motivation for further improvement in the field of teaching. This article presents a developed model of a methodological system for organizing the research activity development in training the future biologists at the pedagogical university. Based on the model, we have developed a comprehensive program for student’s research competence development, which was tested at two courses of a pedagogical university. Comparison of the nine experimental groups (220 students) and nine control groups (218 students) showed that our program designed to develop student’s research competence is effective. The paper also discusses the conditions, under which the program is effective, in particular, the importance of continuing education of teacher educators, as well as the necessity of interaction between educational and scientific institutions.