Exotic plants have been found to use allelochemicals, positive plant-soil feedbacks, and high concentrations of soil nutrients to exercise a competitive advantage over native plants.  Under laboratory conditions, activated carbon (AC) has shown the potential to reduce these advantages by sequestering organic compounds.  In a previous study, the cover of two dominant exotics, Bromus tectorum and Centaurea diffusa, decreased and the cover of two dominant native grasses increased in AC-treated plots relative to control plots, two years after treatment application.  Activated carbon in that study was found to decrease N cycling rates, but the effects on microbial communities remain unknown.  Here we report that the AC treatments continue to suppress non-native plant growth and encourage native grass growth five years after treatment applications.  We also show that AC treatments decrease microbial abundance and diversity.  Of 34 common phospholipid fatty acids extracted from whole soils, 10 were nearly absent from AC-treated soils.  More specifically, AC addition reduced the abundance of fungal and microeukaryote-specific lipids while having less of an effect on gram positive-specific lipids.  This suggests that these fungi and microeukaryotes decrease native grass growth or increase B. tectorum and C. diffusa growth.  Resolving the exact mechanisms through which AC addition to soils changes plant growth is likely to produce new approaches to managing plant communities.