Intercropping the alleys of agroforestry systems is desirable to provide income from the field until the tree crop begins to yield. However, cultivation of annual crops in the alleys may decrease soil organic matter and increase soil erosion especially on sloping landscapes. Perennial crops maintain a continuous soil cover that, combined with trees, maximize water infiltration, minimize soil erosion, and improve overall soil quality. The objective of this on-farm study was to assess the effects of a perennial legume, kura clover (Trifolium ambiguum), on various soil quality parameters in a recently established pecan (Carya illinoinensis) plantation. The pecan-kura clover agroforestry system was established on the Kussman Pecan & Cattle Farm in Chariton County, Missouri on deep loess soils of the Menfro-Higgensville-Wakenda association. These silt loams are on 3 to 10% slopes and are subject to erosion. Kura clover was selected for intercropping in the eight-year-old pecan plantation based on its perennial growth habit, nitrogen-fixing ability, winter hardiness, high quality forage, and soil conservation properties. Kura clover was seeded in 1999 and since 2001 has been annually harvested for hay. During this period soil organic matter and activities of selected soil enzymes (dehydrogenase, glucosidase, glucosaminidase) have steadily increased compared with cultivated and grass pasture control soils. Water-stable aggregation has improved by 50% during this period. Results to date illustrate that kura clover as the interplanted component of this pecan agroforestry system has improved soil fertility and biological activity through increased organic matter, improved soil structure through increased soil aggregation, and has yielded a high quality forage valuable for the cattle-feeding operation. Pecan trees thrive in this system partly because, unlike other “living mulch” systems in which the cover crop suppresses growth of the main crop, kura clover does not compete with tree growth.