Appropriate methodological innovation during a research project in social science is well accepted even when research questions are to be investigated under assumed context. Innovation in research design may lead to changed objectives and expected outcome. In mixed methods research, the elements of both qualitative as well as quantitative research approach are used. I have been conducting a study on women work participation, assets ownership, and empowerment. The purpose of integration of mixed method research design in my research is to support the finding from quantitative data analysis and validate the conclusion drawn with the help of qualitative analysis for 30 International Journal of Qualitative Methods better insight. Case studies and in-depth personal interviews method incorporated in the modified research design, keeping in mind the factors such as social conditioning and upbringing of respondents, is equally important to understand their current context. Through this paper, I would like to discuss challenges faced in integrating mixed method during later phase of research. Some of these challenges are realigning research design with expected outcome, recognizing sample for case studies, personal interviews, categorizing cases based on typology, coding, transforming qualitative data into values for validation of findings, and issues related to biases and prejudices of the investigator.