Studies on teacher preparation highlight the importance of practical experiences such as internships in adequately preparing pre-service teachers for the demands of the profession. However, there has been a lack of focus on the specific difficulties encountered by pre-service physical education (PE) teachers during internships. This study utilized qualitative methods to examine the specific obstacles encountered by eight pre-service physical education teachers while completing their internships at private secondary schools in the northern region of the Philippines. Through thematic analysis of weekly reflective journals, four main themes were identified: personal well-being and emotional strain, classroom management and student interactions, instructional practices and pedagogical challenges, and school environment and institutional factors. The results emphasize the importance of integrating well-being strategies into PE teacher education programs, improving PE-specific classroom management training, and promoting stronger partnerships between universities and schools to offer consistent support, resources, and practical experiences for future teachers navigating the complexities of the PE teaching environment. These findings contribute to a deeper understanding of the experiences of pre-service PE teachers and provide practical suggestions for enhancing teacher preparation and support systems.