Air stripping is commonly used to remove the ammonia in multistage treatment systems for municipal landfill leachate (LFL). This paper proposes a novel approach combining the process of stripping with biological removal of ammonia, based on simultaneous nitrification and denitrification (SND) in a single hybrid sequencing batch reactor (HSBR). To avoid the accumulation of free ammonia (N-FAN), the shallow aeration system was used for the treatment of raw LFL with N-TAN level of 1520 mg/L and pH 9.24. The mean N-FAN removal efficiency of 69% with the reaction rate of 55 mg L−1 h−1 and mean ammonium (N-NH4+) removal efficiency of 84% with the reaction rate of 44 mg L−1 h−1 were achieved within a month in such an HSBR (R1). The comparative HSBR (R2), with conventional aeration system maintaining the same concentration of dissolved oxygen (DO ≤ 1 mg/L), was removing only trace amounts of N-FAN and 48% of N-NH4+. The quantitative analysis of 16S rRNA genes indicated that the number of total bacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Beta- and Gammaproteobacteria increased during the operation of both HSBRs, but was always higher in R1. Moreover, the bacterial community shift was observed since the beginning of the experiment; the relative abundance of Firmicutes, and Beta- and Gammaproteobacteria increased by 5.01, 3.25 and 9.67% respectively, whilst the abundance of Bacteroidetes and Actinobacteria decreased by 15.59 and 0.95%. All of the surveyed bacteria groups, except Gammaproteobacteria, correlated significantly negatively (p < 0.001) with the concentrations of N-NH4+ in the outflows from R1. The results allow us to suppose that simultaneous stripping and SND in a single reactor could be a promising, cost-effective and easy-to-operate solution for LFL treatment.