Pruning an apple tree is essential to good health and fruit production. Too many branches inside the tree will cause less light to enter, making fruit small or inhibiting fruit production altogether. Clogged insides also prevent the tree from drying after wet weather, creating the perfect conditions for fungal infection. Dwarf apple trees may fall over in strong wind if not pruned regularly to remove weight from the base, according to the University of Utah. Pruning during the tree's dormancy will keep the tree healthy and strong.
Prune the tree back to a height of 30 to 36 inches when planting to make the tallest central bud the leader of the tree, creating a strong trunk. Inspect the tree every 4 to 6 weeks to ensure it is still the leader.
Select the three to five healthiest lateral branches from the leader to keep during the tree's first dormancy period. Remove the rest. Place spreaders on the branches if they are facing too vertical to guide them in growing outward.
Remove any fruit from the tree during the third spring to aide the tree in growth. Fruit can break branches or steal resources needed elsewhere by the tree.
Cut the leader back to the desired height once the tree begins bearing fruit. Cut the leader annually to train the tree to the correct height.
Remove any branches that cross each other or are broken during the dormancy period in proceeding years.
Cut away branches from the canopy of the tree to let light inside the tree. Cut away branches using a lopper. Never remove more than 1/3 of the canopy in a season to prevent disease and weakness in the tree.