Leguminous green manure (GM) is a nitrogen (N) resource that can replace chemical fertilizers (CFs) in rice production. The pattern of N mineralization from GM, which changes according to species, growth stage, and the timing of incorporation, affects rice growth and yield. Thus, the characteristics of N mineralization should be clarified to promote the appropriate use of GM. The objectives of this study were to clarify the patterns of N mineralization from flowering- and maturity-stage GMs under flooded conditions after different upland periods, and to evaluate the denitrification loss occurring during the upland periods. Nitrogen mineralized from three species of GMs collected at both the flowering and maturity stages was measured through incubation tests. The three species were hairy vetch (HV), crimson clover (CC), and white clover (WC). The incubation tests included five upland periods (0, 1, 2, 3, and 4 weeks) at 20°C, and each upland period involved eight flooded periods (0, 1, 2, 4, 6, 8, 12, and 16 weeks) at 30°C. The percentage of mineralized N to total N input from the GMs after being flooded for four weeks until after 16 weeks was 1% for flowering-stage HV and 3% for flowering-stage CC, whereas the percentage increased to 41% for maturity-stage HV and 58% for maturity-stage CC. The results indicate that maturity-stage HV and CC slowly mineralize N until the late growth stage of rice. The denitrification loss under upland conditions increased markedly when the upland period extended longer than two weeks. Said loss can likely be attributed to the easily mineralizable fraction of N in the GMs, which is mineralized until having been flooded for four weeks. Thus, maturity-stage GMs, which have a higher C/N ratio than flowering-stage GMs, are advantageous in reducing the denitrification loss during the upland period.