Prune a magnolia tree after its first flush of blooms to avoid inadvertently removing flowering branches, and prune trees that bloom all season long early in the growing season. Don't remove more than one-third of the tree at a time, as over-pruning stresses the tree, and open cuts invite pests.
Prune by removing yellowish or brown wilted leaves and branches. Use a sharp, clean utility knife, and cut into the tree's bark to determine the green location to cut back to when pruning. Wipe the blade after each cut to prevent the spread of disease. A green color underneath the bark indicates growth.