This dataset contains the quantified measurements of greenhouse gas emissions (CO2 and CH4) from dung pats collected to evaluate the effects of ivermectin on dung beetles and prokaryotic assemblages in Mediterranean pastures, based on field experiments conducted under controlled conditions. The treatments either allowed or excluded dung beetle colonisation of dung pats treated with ivermectin or left untreated, while also examining temporal changes in the richness and taxonomic composition of dung-associated prokaryotic assemblages during the first 48 hours after dung deposition. The data show that greenhouse gas emissions at least double in the absence of dung beetles, reinforcing the causal link between ivermectin use and increased CO2 and CH4 emissions. The dataset also shows that the bacterial phyla Firmicutes, Bacteroidota, and Proteobacteria dominated the dung microbiota, with ivermectin potentially favouring certain anaerobic and facultative taxa.