A pre-treatment system, circulation tank was proposed for residual rubber removal from natural rubber (NR) wastewater. The main treatment system consisted of an anaerobic baffled reactor (ABR) and a down-flow hanging sponge (DHS) reactor. An additional DHS reactor (post-DHS) was installed after ABR-DHS system as a post-treatment for nitrogen removal. In the pre-treatment circulation tank, the contact numbers with seed rubber was considered a key factor in the coagulation of residual rubber. Furthermore, the aerobic conditions enhanced the NR wastewater biodegradability in both ABR and DHS reactors. The post-DHS achieved single-stage nitrification-denitrification, using sodium acetate solution as a carbon source, under non-aeration conditions. Finally, the water quality of the final effluent met the quality standards of NR producing countries. In the ABR, hydrogen-utilizing methane-producing archaea, as well as syntrophic VFAs degrading bacteria, were the main bacteria contributing to the organic matter degradation in NR wastewater. On the other hand, most of the residual rubber in the NR wastewater was degraded in the DHS reactor by aerobic rubber-degrading bacteria (Gordonia).