Inquiries into the impact of second language teacher education on the development of teachers' practices, beliefs, and knowledge have increased substantially in the last few years. However, most studies tend to investigate the process of second language teacher learning over a relatively short period of time, and only limited literature addresses methodological considerations in longitudinal research, making the design of this type of study potentially challenging for researchers. The aim of this paper is to first describe an ongoing project which explores the process of teachers learning to teach English pronunciation over a period of six years. Following an overview of the study design, five major challenges that I have faced while conducting the research project are discussed: (1) design issues; (2) access to teacher-participants; (3) time-related issues; (4) data management; and (5) personal involvement. Included in the discussion are methodological insights I have gained while carrying out the research and several navigational strategies I have used to overcome the aforementioned challenges. The purpose of providing this personal account is to shed light on my own experiences with navigating methodological challenges as a means of empowering researchers in designing and carrying out longitudinal research.