Fertilize the apple tree in spring with organic materials, such as well-rotted manure or compost. Spread the material -- 1 to 2 inches thick -- around the tree in a 3-foot radius.
Prune the interior of the apple tree to allow sunlight in and air to circulate. This helps prevent fungal disease and the need to use fungicides. Prune in January or February and remove dead and broken branches, those crossing over others and any that are growing straight up.
Prevent aphid, scale and spider mite infestations by spraying the apple tree with dormant oil before it begins turning green. Spray branches, stems and the trunk until the product drips.
Protect the apple tree from borers by painting the trunk with a 1 percent neem oil product. Apply the oil in June and reapply in late July, according to label instructions.
Spray pure neem oil on the apple tree every 10 days from late spring to harvest.
Clean the soil around the tree of fallen leaves and fruit that act as a safe harbor for pests and fungal pathogens.