The study was conducted to investigate the effect of conflicts on project team productivity at Mastermind Tobacco Kenya Limited in order to build everlasting coexistence of members of a project team and ensure attainment of project as well as overall organizational goal. The objectives of this study were: to examine the effects of project leadership related conflicts on project teams’ productivity, to find out the effects of organizational structure related conflicts on project team productivity and to establish the effects of stakeholder involvement conflicts on project team productivity in Jaza jaza project at Mastermind Tobacco Kenya Limited. A descriptive research design was adopted in this study. The sample was selected through stratified random sampling, study participants were randomly selected from the marketing, finance and human resource departments as they are directly involved in the Jaza jaza project implementation. The target population size was a hundred five respondents and a sample of 45 respondents was drawn. Questionnaires were distributed to the targeted population and duration of four weeks was given. The completed questionnaire was coded, entered into the computer, organized and analyzed with a statistical package for social science (SPSS). The collected data was analyzed and presented in tabular form, graph and chart for simple understanding of the finding and regression analysis was also utilized. In conclusion, the company faces conflicts related to project leadership, organizational structure and stakeholder involvement but to varying extents thus, there is a paramount need to address and manage conflicts to improve on project team productivity as a way to increase the overall performance of the organization. From the study findings, the study recommends that in order to maintain its existence in the market, the tobacco companies should practice conflict management of project teams to boost productivity.