We evaluated soil health in apple (Malus x domestica Borkh.) orchards of New York State. Our objectives were to determine a parsimonious set of biological, chemical, and physical indicators for monitoring orchard soil health, and then to relate long-term management practices to soil health, orchard productivity, and ecosystem services. At one study site, four in-row groundcover management systems (GMS) - pre-emergence herbicide, post-emergence herbicide, mowed sod, and bark mulch - have been maintained in a 0.8 ha orchard for 17 years. Discriminant analysis showed that total soil carbon (%C), organic matter (%OM), and bulk density (g.cm(-3), BD) separated the GMS treatments. The %C and %OM were significantly higher - and BD significantly lower - in mulched plots compared to the other GMS (P<0.05). Previous reports suggest that higher %C and %OM, and lower BD, indicate healthier soil. In regression analyses, %C and %OM positively correlated, and BD negatively correlated, with trunk cross-sectional area, confirming that healthier soils produce larger trees. While high vigor trees are often inefficient fruit producers, this was not observed in our study. Yield was statistically similar across GMS treatments since 2004; yet, there was a trend for trees in the post-emergence herbicide and mulch treatments to yield more than trees in the pre-emergence herbicide and sod treatments. Average pruning weights did not differ among treatments. We cannot conclude that healthier soil translates to higher profits based on yield alone, but system-wide carbon sequestration was significantly higher in the mulch treatment, where soil OM content doubled from 4.5 to 9% over the 17 years of the study. The mulch treatment had statistically higher carbon storage in the soil and in tree biomass. In agricultural programs where best management practices and/or ecosystem services are subsidized, orchard soils with higher organic carbon could be financially rewarded.