Sustainability has become one of the key challenges for Non-Governmental Organizations (NGOs) currently and into the future. Only those institutions that have sound financial structures, stable cash flow flows and proper management will be able to complete their various missions and react to the difficulties that are present in a setting that is becoming more complicated and global. NGOs must make every effort to broaden their funding sources in an effort to increase their autonomy, as well as to broaden and strengthen their base of support so they could use it for both membership dues and volunteer work. This study sought to assess the effect of organizational factors on sustainability of Non-Governmental Organizations in Kenya. Specifically, the study assessed the effect of funding, stakeholder involvement, Capacity building and technical expertise on sustainability of NGOs in Kenya, a case study of Heart-to-Heart Ministry located in Nairobi County, Kenya. In this study, exploratory research design was used for a population totalling 61 comprising management and staff. Since the population was small, sampling was not carried out. Primary and secondary data was collected for this study. Primary data was collected using a questionnaire and interview schedule while secondary information was gathered from NGOs and other documented literature. The collected data was analysed using both quantitative and qualitative data analysis methods. Descriptive tools such as frequencies and percentages were used to present the data. With the help of the Statistical Package for Social Science, data was coded and analysed (SPSS V 21.0). The study tried to determine whether funding, stakeholder participation capacity building and technical expertise have an influence on sustainability of NGOs in Kenya. The findings of the study will benefit the management and policy makers of NGOs with regard to improved sustainability. The study will also contribute to the body of knowledge that will be helpful to scholars interested in the topic in the future