Surface heterogeneity is a major soil characteristic in Niger. Some forms of surface heterogeneity in agricultural fields are known to have intrinsic unfavorable characteristics for soil fertility and agricultural production. The aim of this study was to assess the effect of organic fertilization on soil quality and the production of the KVX 61.1 cowpea variety in constrained areas in the south of the Tillab´eri region and in the far north of the Maradi region. These surface entities are those linked to erosion crusts (ERO) and structural crusts (ST-SN). A total of 56 soil samples were collected before and after application of organic fertilizer for physicochemical analysis in a randomized block design with 6 replicates per treatment implemented in three fields at each site. In this experimental design, cowpea growth and yield parameters were measured, namely nodules, haulm and grain yields. Results showed that the application of organic fertilizer on ERO and ST-SN resulted in a 3- to 6-fold increase in nitrogen, phosphorus, exchangeable bases and CEC, and a correction of soil acidity. Nodule development increased significantly with the addition of organic fertilizer (p< 0.0001), with values ranging from 0 to 230 nodules per plant. Hull and grain yields were higher on the ERO + manure and ST-SN + manure amended areas, with values ranging from 500 kg/ha to 2,300 kg/ha for hulls and 400 to 940 kg/ha for grain, than on the ERO and ST-SN control areas, where values were almost nil. These results will enable to take better account of soil surface heterogeneity in the search for solutions to improve cowpea production.