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In this paper we address the issue of governance quality in the microfinance sector in the Economic and Monetary Union of West Africa and try to build an aggregate index for measuring the sustainability of these institutions focusing on the Benin case study. Following the recent literature on corporate governance in the classic bank sector (Louizi, 2006; Marsal and Bouaiss, 2007), some studies show evidence of a strong correlation between the governance quality of microfinance organizations and their performance (Rock et al., 1998; Labie, 2001; Drake and Rhyne, 2002; Mersland and Strøm, 2007). And governance quality increasingly tends to become the biggest challenge faced by most microfinance organizations in EMUWA. Despite the many facets of governance quality, the analysis of the aggregate indexes built using data from Benin shows that governance quality in the whole sector has been deteriorated. All other things being equal, this conclusion tends to reduce the prospects of viability in the sector. JEL Classification – G21, G30, L31, O55.