Roots influence microbial decomposition of organic matter. We investigated how roots influence decomposition of a simple and complex carbon (C) substrate in mesocosms in a field experiment. Mesocosms were PVC lined with mesh that varied in size, which manipulated root access to soil and produced a gradient of root density. Mesocosms either received an injection of water (control), 13C labeled starch or 13C labeled leaf material. We collected gas samples from the mesocosms and analyzed 13C-CO2, microbial biomass, and enzyme activity. Our empirical data set was compared to a rhizosphere simulation model, CORPSE, to evaluate two alternative model hypotheses: 1) microbes are generalist decomposers, and 2) microbes have different affinities for substrates and may be influenced by roots differently. Our field experiment was conducted in 2014 at Marcell Experimental Forest, MN, USA. We installed mesocosms in May and after six weeks we injected water or substrates into soil. Gas samples were collected 1, 2, 3, 4, 5, 10, 20, and 40 days after injections. Mesocosms that received the starch substrate were harvested from the field 5 days after injections and those receiving leaf material were harvested 40 days after injections. Half of the water-control mesocosm were harvested 5 and 40 days after injections to pair with the substrate mesocosm harvests. Our results suggested decomposition of leaf material was more sensitive to root density than starch. The CORPSE model simulations with microbe-substrate affinity (hypothesis 2) showed a similar pattern to the field experiment. One way that roots influence microbial decomposition is through alleviating C limitation via exudates. Overall, our results suggest that microbial decomposition of starch is not a C limited process and that root density does not alter the rate of starch decomposition. On the other hand, decomposition of more complex substrates such as leaf tissue, which contains cellulose, hemi cellulose, and lignin, may be more C limiting and therefore more sensitive to roots and root exudates.