Anammox and deammonification processes under different five-day biochemical oxygen demand (BOD5) to total nitrogen (TN) ratios (0, 0.1, and 0.2) were investigated in a lab-scale anaerobic sequencing batch reactor (ASBR) and full-scale moving bed bioreactor (MBBR) and integrated fixed-film activated sludge (IFAS) systems operated under different conditions (dissolved oxygen (DO) concentrations, solids retention time (SRTs), organic and ammonia-nitrogen (NH3-N) loading rates). Nitrogen removal efficiencies for the lab-scale ASBR anammox process using synthetic wastewater as substrate and two full-scale deammonification processes (MBBR with anaerobic digester centrate as substrate and IFAS with stored landfill leachate as substrate) were >90%, ∼60%, and ∼75%, respectively. Quantitative polymerase chain reaction and polymerase chain reaction-denaturing gradient gel electrophoresis were used to investigate microbial communities on three different attached-growth media: scrub sponges (ASBR), AnoxKaldnes K5 (MBBR) and polypropylene (IFAS). The anammox species, Candidatus Brocadia fulgida was dominant only in the lab-scale anammox system and Candidatus Kuenenia sp. was dominant under DO concentration of 0.3 mg l−1 and organic loading of 0.04 kg-BOD·m−3·d−1. Candidatus Jettenia caeni was dominant at BOD5:TN ratio of 0.2 and organic loading up to 0.39 kg-BOD·m−3·d−1 and NH3-N loading 1.95 kg-N·m−3·d−1. Furthermore, abundance of amoA-AOA populations in lab-scale and two full-scales treatment systems were similar (around 8.04 × 104 to 1.56 × 105 copies/g-sludge) but different predominant AOA species were observed on the different media. Based on the results from this work, maintaining low BOD5:TN ratios could be applied to improve the nitrogen removal efficiency of deammonification processes. While very low BOD5:TN ratio was the primary determinant of deammonification efficiency, other beneficial influences include high specific surface area carriers, low DO concentration, high temperature, and long SRT.