Integrating cover crops into rotation has many soil health benefits but limited research has examined the effects on microbial-driven biogeochemical cycling. Despite a previously observed increase in microbial abundance due to the inclusion of radish-rye cover crops, we found no significant impact on mineralizable C. Further, we did not observe a change in the thermodynamic efficiency of glucose use or substrate induced respiration following the addition of glucose or alanine; however, there was greater substrate induced respiration in response to glycogen from radish-rye cover crops, suggesting that microbial communities may be better adapted to decompose more complex carbon substrates.