This study evaluated the effects of in-row groundcovers (bare ground, brassica seed meal, cultivation, wood chip mulch, legume cover crop, and non-legume cover crop) and three compost rates (48, 101, and 152 kg available nitrogen (N)/ha/year) on soil carbon (C) pools, biological activity, N supply, fruit yield, and tree growth in a newly planted apple (Malus domestica Borkh.) orchard. We used nonlinear regression analysis of C mineralization curves to differentiate C into active and slow soil C pools. Bare ground and cultivation had large active soil C pools, 1.07 and 0.89 g C/kg soil, respectively, but showed little stabilization of C into the slow soil C pool. The use of brassica seed meal resulted in increased soil N supply, the slow soil C pool, and earthworm activity but not total soil C and N, fruit yield, or tree growth. Legume and non-legume cover crops had increased microbial biomass and the slow soil C pool but had lower fruit yield and tree growth than all other groundcovers regardless of compost rate. Soils under wood chip mulch had elevated earthworm activity, total soil C and N, and the slow soil C pool. Wood chip mulch also had the greatest cumulative C mineralization and a high C:N ratio, which resulted in slight N immobilization. Nevertheless, trees in the two wood chip treatments ranked in the top four of the 13 treatments in both fruit yield and tree growth. Wood chip mulch offered the best balance of tree performance and soil quality of all treatments.