Rake up the fallen, diseased leaves and discard them in the trash. Do not leave them near the plum trees because this encourages the spread of the fungus.
Remove diseased branches and twigs with a pair of pruning shears. Disinfect the pruning shears after use with hydrogen peroxide, rubbing alcohol or bleach to prevent the shot hole fungus from spreading to other plum trees. The disease overwinters in affected twigs and branches, which ooze the bacterium from any lesions, spreading the disease to other parts of the tree, according to the Nebraska Department of Agriculture.
Apply a chlorothalonil fungicide to the infected plum tree when the petals begin to fall in the late spring or early summer. Do not wait so long to apply it that the flowers that cover the immature plums begin to fall off. Control shot hole fungus on a long-term basis by applying chlorothalonil once every year.
Apply a fertilizer in the early spring to reinvigorate your plum trees and help it recover from pruning. Use a well-balanced fertilizer like 10-10-10. Give each plum tree 8 ounces of the fertilizer per year of growth. For example, if your plum tree is 2 years old, give it 16 ounces.