Methane (CH4) emissions from natural systems are rising in a concerning manner with an incomplete understanding of its drivers. Recently, chemical stressors such as antibiotics have been suggested as a thus far overlooked factor increasing methanogenesis in freshwaters. Since usage and toxicological impact of antibiotics could increase in a warming climate, we assessed the temperature-dependence of antibiotic effects on methanogenesis. In this light, we conducted anaerobic incubations with freshwater sediment at 10, 15, and 20 °C in presence of a mixture of five antibiotics at field-relevant concentrations. Weekly measurements of CH4 showed a strong temperature dependence of antibiotic effects by changing effect sizes, directions and dynamics. While antibiotics reduced CH4 production at 10 °C, methanogenesis was elevated at 15 °C with the most pronounced increase occurring at 20 °C. Furthermore, antibiotics changed the prokaryotic assemblage at all temperatures and effect patterns of CH4 producing Methanomicrobia strongly followed the patterns observed for methanogenesis. While analyses of compound-specific stable isotopes and the metatranscriptome suggest the acetoclastic pathway as most relevant, linking prokaryotic structure to function remains one of the most significant research challenges. Nevertheless, the evidence provided by this study suggests a positive relationship between temperature and the stimulating effects of antibiotics on CH4 production.