Over the past century, overgrazing and drought in New Mexico’s Jornada Basin has promoted the replacement of native black grama (Bouteloua eriopoda Torr.) grass communities by shrubs, primarily mesquite (Prosopis glandulosa Torr.). We investigated the effects of shrub expansion on the distribution, origin, turnover, and quality of light (LFC) and heavy (HFC) soil organic matter (SOM) fractions using δ¹³C natural abundance to partition SOM into C₄ (grass) and C₃ (shrub) sources. Soil organic matter beneath grasses and mesquite was isotopically distinct from associated plant litter, providing evidence of both recent shrub expansion and Holocene plant community changes. Our δ¹³C analyses indicated that SOM derived from mesquite was greatest beneath shrub canopies, but extended at least 3 m beyond canopy margins, similar to the distribution of fine roots. Specific ¹⁴C activities of LFC indicated that root litter is an important source of SOM at depth. Comparison of turnover rates for surface LFC pools in grass (7 or 40 years) and mesquite (11 or 28 years) soils and for HFC pools by soil depth (∼150–280 years), suggest that mesquite may enhance soil C storage relative to grasses. We conclude that the replacement of semiarid grasslands by woody shrubs will effect changes in root biomass, litter production, and SOM cycling that influence nutrient availability and long-term soil C sequestration at the ecosystem level.