In the semi-arid zones of West Africa, the relationships between organic matter management methods, soil quality who has resulted and cotton production, remains little or poorly known. In a simple non-randomized block design located at Boni in western Burkina Faso, we studied the impact of three organic matter management methods on soil quality and cotton yield over a period of thirty years. The three modes of crop residue management compared were: extensive management, where residues are exported (SI); semi-intensive management (SII); and intensive management of crop residues (SIII), corresponding to compost and recycled manure inputs respectively. The results showed that, over time, cotton yields and rainfall fluctuated almost identically, whatever the crop residue management method. In terms of soil chemical properties, compost (7.16 g.kg-1) and manure (6.75 g.kg-1) reduced the degradation of soil fertility compared with the initial soil (7.70 g.kg-1). Investigation into the determinants of cotton production at farm level showed that the factors controlling cotton yield are major elements (C, N, Pas and Kt), exchangeable bases (Ca2+, Mg2+, Na+ and K+) and CEC. Regardless of how soil fertility is managed, cultivation has led to a decline in soil fertility. This study served as a reminder of the benefits of good agricultural practices for sustainable soil fertility management.