Zeolite addition has been widely suggested for its ability to overcome ammonia stress occurring during anaerobic digestion. However little is known regarding the underlying mechanisms of mitigation and especially how zeolite influences the microbial structuration. The aim of this study was to bring new contributions on the effect of zeolite on the microbial community arrangement under a low ammonia stress. Replicated batch experiments were conducted. The microbial population was characterised with 16S sequencing. Methanogenic pathways were identified with methane isotopic fractionation. In presence of ammonia, zeolite mitigated the decrease of biogas production rate. Zeolite induced the development of Izimaplasmatales order and preserved Peptococcaceae family members, known as propionate degraders. Moreover methane isotopic fractionation showed that hydrogenotrophic methanogenesis was maintained in presence of zeolite under ammonia low stress. Our results put forward the benefit of zeolite to improve the bacteria-archaea syntrophy needed for propionate degradation and methane production under a low ammonia stress.