Three long-term apple (Malus x domestica Borkh.) orchard management systems were evaluated in 2007-2008 for effects on soil health, orchard productivity, and carbon storage. The treatments were as follows: tree-row pre-emergence herbicide, post-emergence herbicide, sod, and bark mulch in a groundcover management systems (GMS) study; integrated and organic fruit production (IFPOFP); and pre-plant compost or fumigation and rootstocks 'CG.6210' and 'M.26' in an apple replant disease (ARD) site. In the GMS study, bark mulch groundcover improved biological, chemical, and physical soil health in the sixteenth and seventeenth years of this study, compared to the other three treatments and commercial orchard averages, which were evaluated in 2008-2009. Total carbon was an important indicator of soil health at this site. Improvements in soil health in the mulch treatment translated into larger tree size and greater system-wide carbon storage, but not to higher cumulative yield, which was similar to that of the postemergence herbicide treatment. Integrated fruit production - which had bark mulch groundcover, compared to cultivation weed management in the OFP - had greater biological activity but similar chemical and physical soil characteristics as the OFP in the fourth and fifth years of this study. Leaf nitrogen was low in both treatments, and tree size and carbon storage were similar for the two systems. Nevertheless, cumulative yield was greater in the IFP. Vesicular arbuscular mycorrhizae spore count and soil respiration were important indicators of soil health, and these indicators correlated positively with cumulative yield. In the ARD study, pre-plant compost improved soil chemical properties compared to pre-plant fumigation, with available soil calcium and phosphorus being important indicators of soil health. Pre-plant treatments had no effect on tree growth and yield by the sixth and seventh years of this study, but growth and yield were greater with rootstock 'CG.6210' compared to 'M.26'. Pre-plant compost and rootstock 'CG.6210' improved carbon storage in this system. This work illustrates the effects of management on orchard productivity and sustainability.