Relevance. This study addresses the need for a new methodological system to meet the current demands of natural science teacher training in schools in Kazakhstan. The effectiveness of this system should align educational objectives with outcomes. Purpose. The aim is to equip future teachers with skills to convey scientific information to pupils of various age groups, introduce methods and teaching configurations to enhance educational activities and apply development methods. Methodology. The study involved theoretical analysis and synthesis of philosophical and educational psychology literature, modelling, observation, and analysis of future teachers' activities. Results. The research investigated and systematised approaches to methodological design in educational programmes, identifying key professional competencies. It established factors of professionalism to form mental models of professional activity and self-concept in individuals. Conclusions. The study highlights the necessity for a revised methodological system to enhance natural science teacher training in Kazakhstan. It emphasises aligning educational objectives with outcomes and equipping future teachers with the skills to communicate scientific information to students effectively. The research has established the importance of integrating modern methods and teaching configurations to foster educational activities. Additionally, it underscores the relevance of developing professional competencies and mental models for professional activity. The findings support the development of educational programmes that address current educational reforms and the interdisciplinary nature of modern science, promoting a comprehensive approach to teacher training in natural sciences. Keywords: innovation process; teacher education; development of educational programmes; methodological system