Anaerobic digestion (AD) of swine waste allows obtaining renewable energy, biofertilizer and the reduction of environmental impacts. However, the low C:N ratio of pig manure generates high concentrations of ammonia nitrogen in the digestion process, reducing methane production. Zeolite is an effective ammonia adsorbent; thus, in this research the ammonia adsorption capacity of natural Ecuadorian zeolite was studied under different operating conditions. Subsequently, its effect on methane production from swine waste was evaluated using three doses of zeolite, 1.0, 4.0 and 8.0 g, in 1 L batch bioreactors. The results showed that the Ecuadorian natural zeolite has an adsorption capacity of around 19 mgNH3-N gZ−1 when using ammonium chloride solution and, an adsorption capacity between 37 and 65 mgNH3-N gZ−1 using swine waste. On the other hand, the addition of zeolite had a significant effect on methane production (p < 0.01). The zeolite doses that provided the highest methane production were 4.0 and 8.0 g L−1, which led to values of 0.375 and 0.365 Nm3CH4 kgVS−1, compared to the values of 0.350 and 0.343 Nm3CH4 kgVS−1 that were obtained for the treatments without addition of zeolite and using a dose of 1.0 g L−1, respectively. Addition of natural Ecuadorian zeolite meant not only a significant increase on methane production in the AD of swine waste, but also a better quality of the biogas with higher percentages of methane and lower concentrations of H2S.