For an apple tree, how many inches above the soil should I keep the graft union after planting?

For trees on size controlling rootstocks, the bud union should be 3 to 6 inches above the soil line. Remember that in some instances the tree can settle causing the bud union to become covered with soil. If the union is covered it may allow the scion to develop roots and the benefits of the size controlling rootstock could be lost. Conversely if the union is too high you may experience increased size control resulting in a smaller tree than desired. For fruit trees that are not on size controlling rootstocks you should plant trees to the depth they were planted in the nursery, which is usually just below the bud union.

Answer provided by Rob Crassweller, Penn State University.