Monitoring and Evaluation over time have gained traction and become fundamental components in projects. Most internal evaluations are based on the assumption that evaluators are independent and do not bow to different forms of influence. Literature however reveals cases of evaluators being confronted by stakeholders to either alter or misrepresent their findings. Independence of evaluators at work is therefore at stake. The fear is that unless a solution is found, interferences are likely to continue hence threaten the credibility of evaluations. Empirical studies have been conducted on factors affecting monitoring and evaluation; these studies however do not adequately address lack of evaluation independence. Since most organizations build evaluation capacity with the aim of improving monitoring and evaluation, this study focused on investigating the effect of capacity building on evaluation independence as a way of addressing the empirical gap so as to safeguard evaluations. The broad aim of this study was to determine the effect of evaluation capacity building on evaluation independence among Public Benefit Organizations in Homa Bay County, Kenya. The specific objectives of the study were to determine the effect of monitoring and evaluation financing, stakeholder participation, staff development and evaluation environment on independence of evaluation among those Public Benefit Organizations. The research design used was descriptive. The target population comprised 39 Public Benefit Organizations in Homa Bay County. Given the relatively small target population, the study used census method hence enrolled all the 51 monitoring and evaluation staff working in the 39 organizations to serve as respondents. Qualitative data obtained was grouped into themes and explored by content analysis whereas quantitative data was analyzed using Statistical Package for Social Sciences. Descriptive analysis generated; frequencies, percentages, means and standard deviations which were presented in tables and charts and interpreted. For Inferential analysis; Pearson‟s correlation and multiple regression were used to establish the effect of evaluation capacity building on evaluation independence at 0.5 significance level. The study revealed that three of the four evaluation capacity building aspects that is: monitoring and evaluation financing, stakeholder participation and evaluation environment all had positive and significant effect on evaluation independence. Regression analysis however found that staff development have no significant influence on evaluation independence. Based on the overall study objective, the findings led to a conclusion that evaluation capacity building significantly affects evaluation independence. The study therefore recommends that Homa Bay County Public Benefit Organizations invests more in capacity building as a prerequisite for credible evaluations, consider separating their evaluation functions from other management functions, increase the number of monitoring and evaluation staff to avert the shortage as well as devise proper strategies for stakeholder involvement in their evaluations.