Aims: This study was undertaken to assess the influence of seed treatment (soaking in water) on nutritional and microbiological composition of two cowpea cultivars. Place and Duration of Study: Laboratory of Food Biochemistry and Tropical Products Technology, and the laboratory of Biotechnology and Food Microbiology, University of Nangui Abrogoua, Abidjan, between October 2010 and December 2011. Study Design: Method based on AOAC tests and AFNOR for microbiological analysis. A two-way analysis of variance and t-test were used. Methodology: The proximate composition of soaked and non soaked cowpea grains was determined and microbiological (bacteriological and mycological) analysis of these grains was also performed. Results: The major components were 28% and 26.25% protein, 48.35% and 47.99% carbohydrate, 41.66% and 40.05% starch for the RC (red cultivar) and WC (white cultivar) respectively. Lipids are less represented in the 2 cultivars (2.5%). There were significant reductions in the contents of the major components as a result of the treatment. Plain water soaking brought about a significant decrease in the proximate composition causing a mean reduction of 3.14% and 10.02% protein, 28.23% and 29.30% carbohydrate, 29.47% and 28.94% starch, 18.80% and 22.02 % energy for the RC and WC respectively. The mean decrease for mineral was 23.13% and 47.66% iron, 2.32% and 8.15% calcium, 9.30% and 2.10% phosphorus for the RC and WC respectively. In general the highest reduction was observed in the WC variety. Mean count (Log10 cfu/g) of total aerobic miroflora, coliforms, mould and yeast were 6.29 and 6.43; 2.04 and 2.58; 4.41 and 4.78 for the RC and WC respectively. Five genera of mould were isolated: Aspergillus, Mucor, Penicillium, Botrytis and Geotrichum. The predominant fungi belonged to Aspergillus genus. Conclusion: The cultivar types of cowpea and the preparation methods could affect the nutrient availability of this product. Cold water soaking has a great influence on the properties of cowpea grains.