Faith Based Organizations (FBOs) play a significant role in environmental management in Uganda. Despite this, they have been largely ignored in scholarship leading to a significant gap in understanding activities they carry out and challenges they encounter in environmental management. This study explored the strengths, weaknesses, opportunities and threats associated with environmental management by the FBOs in Uganda. FBOs selected and studied were the Roman Catholic Church, Anglican Church of Uganda, the Muslim Faith, Pentecostal Assemblies of God and the Seventh day Adventist, since they consist over 86% of Uganda’s population. Qualitative and quantitative research strategies with systematic and purposive sampling techniques were used. SWOT analysis using Key Informant Interviews and questionnaires were carried out to obtain information from seven (7) key decision-making staff at the FBOs’ headquarters and 75 from regional centers. Quantitative and qualitative data were analyzed by descriptive statistics and content analysis respectively. Key strengths of FBOs in environmental management include; land ownership, skilled human resources and finances. Existence of good structures from grassroots to national level, knowledge in environmental management and an extensive following countrywide boosts the capacity of FBOs to engage in environmental management activities. Major areas that need improvement are; knowledge and skills in environmental management of leaders and followers; resource mobilisation skills and interest in environmental conservation among most clergy and Imams. Key opportunities were; existence of large number of employees and followers who can be trained in environmental management and the structures from grass-root to national level. Key threats were human population explosion, poverty, land grabbing and unfavourable land tenure and policy changes. FBOs are instrumental in environmental management but are constrained by financial resources, limited knowledge and skills in environmental management and fundraising abilities. This calls for capacity building in these aspects in order to impart the required knowledge and skills to FBOs leaders and followers. Government and other able stakeholders should support FBOs in their endeavor to conduct environmental management activities in Uganda.