Biological desulfurization of biogas from a field-scale anaerobic digester in Peru was tested using air injection (microaeration) in separate duplicate vessels and chemical desulfurization using duplicate iron filters to compare hydrogen sulfide (H2S) reduction, feasibility, and cost. Microaeration was tested after biogas retention times of 2 and 4 h after a single injection of ambient air at 2 L/min. The microaeration vessels contained digester sludge to seed sulfur-oxidizing bacteria and facilitate H2S removal. The average H2S removal efficiency using iron filters was 32.91%, with a maximum of 70.21%. The average H2S removal efficiency by iron filters was significantly lower than microaeration after 2 and 4 h retention times (91.5% and 99.8%, respectively). The longer retention time (4 h) resulted in a higher average removal efficiency (99.8%) compared to 2 h (91.5%). The sulfur concentration in the microaeration treatment vessel was 493% higher after 50 days of treatments, indicating that the bacterial community present in the liquid phase of the vessels effectively sequestered the sulfur compounds from the biogas. The H2S removal cost for microaeration (2 h: $29/m3 H2S removed; and 4 h: $27/m3 H2S removed) was an order of magnitude lower than for the iron filter ($382/m3 H2S removed). In the small-scale anaerobic digestion system in Peru, microaeration was more efficient and cost effective for desulfurizing the biogas than the use of iron filters.