This study elucidates the effects of the projected climate variables and CO2 on yam yield in relation to three major soils in the Upper Ouémé basin (Benin Republic) on yam (Dioscorea alata) yield. The impact of the SRES climate scenarios A1B and B1 based on the output of the GCM ECHAM5 downscaled with the REMO model and the A1B scenario output of the GCM HADC3Q0 downscaled with the RCMs SMHIRCA and HADRM3P were analyzed. The A1B scenario, as expected with highest increase in temperature and extreme decline in rainfall, exhibited a decrease of 33% in yield until 2050 under ambient CO2 concentration (350 ppmv), while under B1 around 27% decline was registered. Whereas, decline under A1B emission scenario of SMHIRCA and HADRM3P accounted 19% and 18%, respectively. The soil type “Ferruginous soils improverished without concretions” (S1) was most sensitive to climate change registering a decline of 48% in yam yield in the decade 2041–2050 followed by “Ferralitic soils” (S2) and “Raw mineral soils” (S3) showing a decline of 36% and 33%, respectively under A1B scenario derived from REMO model. Analysis of the growth constraints suggest that besides water stress, the indirect effect of reduced rainfall on the release of nitrogen from soil organic matter and hence nitrogen deficiency in the yam crop was the major constraint in the S1soil type.