Organic fertilizers may contain cadmium (Cd) and the transformation of organic materials in soil also has a role in soil-plant Cd distribution, both of which lead to Cd accumulation in plant edible parts. However, the advisability of applying organic fertilizer to remediate soils that are moderately and slightly contaminated with Cd has not been clarified. In this study, we investigated the impacts of an organic amendment (chicken manure) on the Cd concentration in rice grains (Cd_R) and the soil chemical properties over a five year period (10 rice seasons) within a slightly contaminated paddy soil in Hunan Province, subtropical China. We found that the Cd_R was reduced by 28%–56% as a result of the organic amendment. The within-year reduction in Cd_R was higher in late rice (43%–56%, averaging 51%) than in early rice (28%–45%, averaging 38%); however, the inter-annual reduction in Cd_R was fairly stable (40%–49%), which suggests that chicken manure amendment has a long-term and persistent remediation potential. The concentrations of DTPA-extractable Cd and exchangeable plus water-soluble Cd fractions in soil were reduced, whereas soil pH and the concentrations of soil organic C and its labile fractions increased. These results indicate a lower apparent phytoavailability of Cd in soil following organic amendment. A two-variable empirical model using DTPA-Cd extracted from the soil at the full heading stage of rice and a climatic factor (total precipitation during the rice growing season) showed great potential in effectively predicting Cd_R. Our study suggests that Cd phytoavailability in soil (indexed by DTPA-extractable and exchangeable Cd) and climatic factors (such as temperature and precipitation) may control inter-annual reductions in Cd_R following organic amendment in slightly contaminated paddy soils.