Nectarine trees need to be pruned to optimize fruit production and allow light into the tree. Most home gardeners do not prune their trees enough. Pruning encourages new growth and shapes the tree.
Prune nectarines hard, removing most of the previous year's growth. Fruit will be produced on the previous year's wood, so leave enough to ensure a good crop, but not overburden the tree. Removing interior branches opens up the tree and allows light to penetrate to lower branches.
Prune nectarine trees when planting to develop three to five lateral branches. Cut transplants with a trunk diameter less than 3/8 inch back to 18 to 24 inches above the ground. On larger transplants, leave three to five well-placed lateral branches and remove other branches. Cut the lateral branches back 2 to 3 inches to stimulate growth.
Prune nectarine trees lightly during the first summer. Remove undesirable branches as they appear, encouraging growth on the chosen lateral branches.
Prune nectarine trees during the first dormant winter season to shape the tree. Prune back the selected lateral branches to 2 to 3 feet from the trunk, leaving small shoots to produce next year's growth. Remove other branches.
Prune during the second winter dormant season to develop secondary lateral branches. Choose two to three healthy branches growing from each of the primary branches. Choose branches growing outward that do not overlap much. Cut these branches back to about 20 to 36 inches from the primary branch, leaving small shoots and twigs along the branch. Remove other secondary branches.
Prune during future winters to open the center and shape the tree. Nectarines grow on last year's wood. Remove excessive growth along the branches, leaving enough to produce the year's crop. Too many shoots will overburden the tree.
Prune away tall branches to keep the tree at an easy height for harvesting. Removing growth from the top will encourage the tree to grow taller.
Remove the pruned branches from the area to discourage pests and prevent disease.