In 1928, Alexander Fleming identified the antibiotic properties of penicillin. Since this discovery antibiotics have been a boon for human health as well as for agricultural livestock production. In fact, the latter utilizes 80% of the antibiotics produced in the United States, a staggering 33 million pounds a year. Most of these antibiotics and antibiotic derivatives ultimately enter the environment, leading to the assertion that no environment on earth is free from the influence of agricultural antibiotics. Despite this, little research has examined the environmental influence agricultural antibiotics are likely to have, for example, on microbial communities and the ecosystem processes they mediate. Here we demonstrate through a series of field- and laboratory-based studies, leveraging next-generation sequencing and stable isotope tracing, that antibiotics can dramatically alter microbial community composition and function. For instance, we show that antibiotics lead to increased abundance of antibiotic resistance genes and shifts in microbial community composition. Additionally, we find that microbial carbon-use efficiency is negatively impacted by exposure to antibiotics. This also leads to decreased ecosystem efficiency (i.e., more carbon is lost via respiration than is reattained within the system) and shifts in the entire food web (i.e., arthropod communities as well as microbial communities). Furthermore, the impact of antibiotics on microbial communities can be exacerbated by other stressors, such as increasing temperature. This leads to more drastic changes in microbial community composition and network structure, and exposure to antibiotics may fundamentally shift the response of microbial communities to global change. In conclusion, antibiotics are an often under-appreciated and diffuse environmental contaminant, but antibiotics have the potential, even at low concentrations, to fundamentally alter microbial communities and ecosystem processes.