The secondary metabolites of milled rice influenced by agronomic practices, seasons and their interaction effects were investigated. The ethanol extracts of rice grains in two japonica cultivars (Taikeng-16 and Kaohsiung-139) were analyzed with different assays to measure the total phenolic content, reducing power, radical-scavenging activity and chelating activity. Similar to earlier studies of phytochemicals, significantly higher antioxidant values were recorded in the organic rice. Second crop (November/December) in comparison with first crop (June/July) had significantly higher values of antioxidant activities, except for the chelating effect. The interaction between the agronomic practices and seasons had a detrimental effect on the crops because the combined factors had a more significant role than each factor alone. Even with the alterations in their content, polyphenols were positively correlated with the antioxidant activities, with the exception of chelating activity, when considering both factors (agronomic practices and season).