Soil carbon (C) is the largest terrestrial reservoir for atmospheric CO2, thus, an increase in soil C can aid in the mitigation of climate change. Soil C storage, litter input and soil microbial communities are intrinsically linked, because soil C storage is controlled by the quantity of soil C input, and soil C losses as controlled by microbial decomposition processes. It is uncertain how the quantity of soil organic matter input affects the soil microbial community structure and subsequently soil C cycling. We assess how litter input rates impact microbial communities and soil C storage in dryland detritus input and removal treatment studies (D-DIRT) in two deserts: Reynold’s Creek Experimental Watershed-ID, vegetation sagebrush (Artemisia tridentate), and Santa Rita Experimental Range-AZ, vegetation mesquite (Prosopis glandulosa). Litter inputs were manipulated at shrub and inter-canopy microsites: control litter, no litter, and double litter. To evaluate impacts of differential litter inputs on soil microbial communities, we collected soils (7.5 cm depth), extracted soil microbial DNA, and conducted qPCR analyses to quantify the relative abundance of fungi and bacteria across the treatments. Our study will allow for a better understanding of the mechanism by which differential litter inputs affect C cycling in arid ecosystems.