The value of tall fescue (Festuca arundinacea Schreb.) for C sequestration in addition to forage production and soil conservation is of current interest. However, studies relating to the impacts of endophyte infected (E+) and endophyte free (E−) tall fescue on soil organic matter fractions are few. This study examined how E+ and E− growth affected soil C fractions 4 years after establishment. The study site was at the University of Kentucky research farm, Lexington, Kentucky, USA. From soil cores in replicated fields we measured total C, particulate organic matter C (POM C), microbial biomass C (MBC), mineralizable C (Min C), C in aggregates, and aggregate distribution at depths of 0 to 15 and 15 to 30 cm. Significant effects between E+ and E- fescue were sometimes observed for MBC, Min C, C in micro-aggregates, and aggregate distribution, but not for total C, and POM C. At 0–15 cm MBC (E+ 26% greater than E−), Min C (E+ 43% lower than E−), C associated with micro-aggregates (E+ 15% lower than E−), and micro-aggregates (46% more micro-aggregates in E+ than E−), were affected by endophyte infection, confirming hypotheses that early changes in soil properties were reflected in labile C fractions and soil structure. Endophyte infection status in tall fescue has quantifiable effects on C sequestration and soil structure, achievable in a relatively short period that can be used to monitor conservation efforts and the consequences of pasture renovation strategies.