This research project examines the challenges faced by Small and Medium Enterprise (SMEs) owners while maintaining the books of accounts within the Thimphu region. First, the study identified the common factors that affected and influenced the book-keeping habits of SME owners globally through various reviews done by other research scholars. After that, the research studied and identified the most common factors among the identified variables (lack of accounting knowledge, time constraint, costly, and lack of training). The research is based on a descriptive study and is targeted for SME owners in Thimphu as it has the highest number of SME businesses registered under the Ministry of Economic Affairs. The data is analyzed using descriptive statistics, one sample T-Test, and Spearman correlation coefficient, and the results are presented in table and figures. A total of 110 SME owners were interviewed and data was collected through a structured questionnaire.