While a properly trained pecan tree does not require much pruning, dead, diseased and damaged wood must be removed for the tree's health as soon as it's noticed. All other pruning should occur late in winter, while the tree is dormant. Additional pruning encourages the development of new wood, which will increase the size of your your pecan crop. If your old pecan tree was trained to a shape, do the best to adhere to that shape while pruning. If your tree was not trained, don't try to shape it. Instead, target and eliminate the types of growth outlined below.
Check over the limbs of your pecan tree for dead, diseased or damaged branches. Diseased and damaged branches should be discolored or physically marred. Dead branches feel light to the touch and do not move in the wind like other limbs.
Combine bleach and water in a 1:10 ratio in a bucket. Place your pruning tools in this bucket.
Strip off dead, diseased and damaged branches at their base. Cut off limbs with a 3/4-inch of smaller diameter with the anvil pruners and larger ones with the lopping shears. If you need to remove large limbs, saw them off with a hand saw.In between each cut, re-wet your pruning tools in the bleach solution. This prevents you from spreading disease through the pecan tree.
Dispose of the bleach solution, and of your dead and damaged wood, when you've removed all of it. Throw the wood in a garbage bin rather than a home compost, since it can spread disease.
Cut off any low-growing limbs that impede movement underneath the tree. Also cut off any limbs that grow downward.
Remove up to one-third of the pecan tree's growth. Eliminate any upward growing limbs that parallel the trunk, since these cast shade. Also cut off limbs that rub up against other limbs, as these can cause pressure damage. Cut away weak shoots as well as older limbs that do not produce much foliage or pecans.