This study empirically investigated the barriers of Microfinance banks’ credit delivery to small enterprises in Nigeria. The areas of study were Lagos and Ogun States. The population of the study was made up of all the Microfinance banks in Lagos and Ogun States in the South –Western Nigeria. A sample of eight (8) microfinance banks were chosen; with five (5) from Lagos State and three (3) from Ogun State using the purposive sampling method. The choice of the sample size was predicated on ability of the researchers to access financial statements of the selected microfinance banks in the two selected states in the South –Western, Nigeria. Primary data was used through a structured questionnaire. Total of forty (40) questionnaires were administered to the respondents, consisting of MFBs staff – branch managers, operation managers, risk managers, and credit officers who examined and administered credit applications from small enterprises’ owners on behalf of bank management on a one-on-one basis. Mean ranking and factor analysis were used to analyze the data. Findings revealed economic recession as major barrier confronting MFBs in credit delivery to small enterprise owners. The study concluded that despite the roles of MFBs to provide loans and other financial services to small enterprises operators, the sector was faced with different barriers thereby limiting their financial performance. The study recommended that Central Bank of Nigeria (CBN) should adopt a holistic approach on how barriers confronting MFBs would be drastically reduced, controlled and managed to improve MFBs operations.