Abstract Constructed wetland (CW) offers a long-term solution for wastewater treatment due to its high nutrient removal efficiencies, ecological benefits and low costs. Similarly, biochar, a carbon-rich organic material, offers a cost-effective solution for enhancing water treatment in CWs while also contributing to carbon footprint reduction. This study was aimed to assess the nitrogen (N) removal performances of Acorus calamus and Cyperus alternifolius in vertical flow constructed wetlands (VFCWs) treating simulated up-flow anaerobic sludge blanket (UASB) reactor effluent, focusing on the role of specific plant species. Rice husk biochar (RHBC) as a substrate material was amended to intensify further organic and N removal efficiencies of VFCWs. Five sets of VFCWs microcosms both planted and unplanted with biochar were developed to investigate the combined effect of biochar and plants on N removal. Results showed that CW1 (C. alternifolius + RHBC) demonstrated the highest total nitrogen (TN) and chemical oxygen demand (COD) removal efficiencies of 83.93 ± 4.70 and 86.70 ± 8.43%, respectively, outperforming the Control and other VFCWs. Nitrogen mass balance showed that, compared to CW3 (A. calamus + RHBC) CW1 achieved ~ 7% higher TN removal, primarily through plant uptake and biochar adsorption. Plant uptake and substrate adsorption were responsible for 30 and 26% of TN removal in CW2 (C. alternifolius) and CW4 (A. calamus), respectively. Furthermore, sequencing of the V3–V4 region of the 16S rRNA gene from sand revealed the highest phyla diversity in CW1, with Nitrosospira detected exclusively in CW1 (0.02%) and CW2 (0.01%), while being undetectable in Control, CW3 and CW4, suggesting a comparatively enhanced microbial richness and potential nitrifying activity in CW1 and CW2. These findings provide insights into the N removal mechanism of different plants and their interaction with biochar for improved N and organic removal in CWs.