As a stable and effective approach for NO2--N accumulation, partial denitrification (PD) could significantly cut down operation cost, and PD/Anammox (PD/A) is a promising nitrogen removal process in wastewater treatment. The biotoxicity of free ammonia (FA) to nitrifying bacteria and anammox bacteria has been demonstrated, while whether FA affects PD bacteria is an open question. Here, long-term operation of PD-fixed bed biofilm reactor (PD-FBBR) treating synthetic wastewater and mature landfill leachate was conducted to reveal the mechanism concerning the effect of FA on PD bacteria. Stable NO2--N accumulation was achieved with NO3--N to NO2--N transformation ratio (NTR) of 60-70% during 280-day operation with FA ranged from 0 to 20.71 ± 0.23 mg/L, while NTR decreased and maintained at ∼30% when FA reached 40.59 ± 0.19 mg/L. Specific NOx--N reduction rate improved at low FA concentration (< 12 mg/L), while high FA level (> 25 mg/L) had inhibitory effect on PD bacteria. Under FA stress, more extracellular polymeric substances (EPS) were secreted, and the glnA gene abundance, glutamine synthase concentration, and glutamine concentration in cell and EPS significantly increased, indicating the enhancement of glutamine biosynthesis in PD bacteria for ammonia assimilation played an important role in response to FA stress. Metagenomic sequencing showed that FA stimulated the upregulation of narK (NO3--N/NO2--N antiporter) gene abundance and enhanced uptake of NO3--N and extrusion of NO2--N. Comamonas, unclassified_f__Comamonadaceae and Thauera were highly enriched in biofilm, which played a key role in the stable NO2--N accumulation. Furthermore, a novel two stage PD/A-FBBR was applied to mature landfill leachate treatment, and satisfactory total inorganic nitrogen removal efficiency ranged from 81.38 ± 3.56% to 89.16 ± 1.57% was obtained at relatively low COD/NO3--N of 2.57-2.84. Overall, these findings demonstrated how PD bacteria respond to FA stress and confirmed the feasibility of PD/A process in high FA wastewater treatment.