Silicon (Si) is known as a beneficial nutrient in the cultivation of rice, playing a key role in photosynthesis enhancement, lodging resistance and tolerance to various environmental stress. The present study aimed to examine available Si content in both lowland soils (n = 29) and neighboring upland soils (n = 21) collected from Benin and Nigeria and to evaluate the validity of the assessment results through a pot experiment. Our results revealed that the acetate-buffer method predicted Si concentration in rice straw at the harvest stage (R2 = 0.68, P < 0.01) better than the anaerobic-incubation method (R2 = 0.31, P > 0.05), and 76% of the uplands and 38% of the lowlands were deficient (< 50 mg/kg) in acetate-buffer soluble Si. These findings suggest that the Si-deficiency soils prevail across the study area, making rice plants starved for Si and prone to environmental stress.