In this study, upland red soils under different fertilization regimes were collected, and soil microcosms supplemented with lignin or milled oyster shell (OS) were established. Isotope tracer and molecular assays were used to evaluate the effects of fertilization and soil amelioration on atrazine mineralization and degrading microbes. The results show that the accumulative mineralization of atrazine is less than 0.33% in soils fertilized with mineral and farm yard manure fertilizers. Milled OS significantly enhances the mineralization of atrazine to 43.3% in the mineral and 9.51% in the manure fertilized soils, respectively, coupled to an increase in soil pH and to changing bacterial communities. Meanwhile, atzC and trzN genes that are responsible for atrazine biodegradation are enriched. In contrast, lignin does not stimulate atrazine mineralization. Instead, lignin considerably increases the formation of nonextractable residues, thus decreases the bioavailability of atrazine. These findings contribute to a comprehensive understanding of environmental fate of atrazine in red soil, and highlight the potential of soil amelioration in mitigating pollutants.