The purpose of this study was to investigate the difficulties pre-service teachers experience in conducting and writing research projects. A concurrent mixed research design was utilized to identify the primary difficulties. To collect the data, the study employed a questionnaire and document analysis. A closed-end questionnaire was administered to natural science candidates of Teacher Education College. The questionnaire data were analyzed using statistical procedures like frequencies and percentages. For document analysis, nine research papers were selected and analyzed by setting evaluation criteria. Two coding cycles (in vivo and axial) were used to evaluate the quality of the papers, and the results were embedded in the quantitative questionnaire. Contrary to the previous findings, the most challenging area candidates struggled with when conducting research was found to be a lack of knowledge and skills in analyzing, organizing, and interpreting data. It was also found that the candidates lacked primarily procedural knowledge and also epistemic knowledge to accomplish research projects. Thus, it was suggested that courses and delivery strategies should include high-level knowledge such as procedural and epistemic knowledge to promote students' problem-solving skills.