Of the over 100 different species and numerous cultivars of magnolia trees gardeners grow, the southern, star and saucer magnolias are likely the most encountered by average homeowners. These trees grow best and with the least issues of pest or disease when in a humus-rich, acidic, moist soil and partial shade to sunny locations. Pruning is best undertaken in late spring so regrowth has ample time to mature before the fall frosts. Since pruning wounds on magnolias tend to be slow to heal, shaping the magnolia when it's young and branch cuts that are smaller, reduces the need for pruning the tree later in life.
Retain the natural architectural shape of the young magnolia tree species in your garden. Consult the nursery invoice or plant tag or do research in garden literature to learn its identity. Most magnolias grow with a singular trunk with tiered, twiggy branches. The star magnolia is a notable exception, commonly developing multiple stems or small trunks to look like a rounded large shrub. When shaping the young tree, you want to maintain this natural habit during the shaping/pruning.
Prune out any damaged or dead branches and twigs from the young magnolia tree whenever encountered. Make the pruning cut with a sharp hand pruner's blades 1/4 to 1/2 inch above a lower healthy branch junction, leaf or dormant bud. When cutting off entire branches, do not cut the branch off flush with the main trunk. Make the cut just above the swollen ring or "collar" at the base of the branch just before it blends into the trunk. Do not cut into the flaring, swollen area of the collar but in the smooth, cylindrical area of the branch's base.
Remove the smaller, weaker branch of any co-dominant branches on the young tree. Co-dominant branches typically form a narrow angle with each other and originate from the same location. Angled branch junctions less than 30 degrees are structurally weak; thinning out the weaker co-dominant branches eliminates limb breakage years later once the magnolia grows substantially.
Trim away any twigs that are rubbing into each other or rubbing onto main branches. Make the cuts of these twigs 1/4 inch above their attachment point on their branches. Also clip off any twigs that are growing inward into the centre of the tree. You want the magnolia's branches to be all outward and upward-growing away from the main trunk or leader at the top of the tree.
Prune away any weak-looking and closely spaced branches on the main trunk once the magnolia tree has grown for two years after planting. According to horticulturists from the University of Kentucky, you want branches to be scaffolded 18 to 24 inches apart on the main trunk. Remember not to prune into the swollen collar neck on branch bases as noted in Step 1.
Tip-prune branches after flowering ends to control the spread or length of branches in the canopy. Make cuts 1/4 inch above a lower leaf, bud or desired branch/twig junction. Keep in mind continually tip pruning a magnolia to keep it small creates many wounds and leads to diminished flowering. Tip pruning helps prevent branches that grow into building facades or into walkway spaces, or those destined in a couple years to grow into another branch or tree nearby.
Choose well-structured magnolia trees at the nursery, not sickly looking or crooked saplings with weedy branching or lots of co-dominant branches. Err on the side of under-pruning a magnolia tree. Generally speaking, magnolias naturally have a good branching structure. Do not over-prune to create many cutting wounds and destroy the overall habit of the plant.
Never "top" or prune off the upright central singular tip of a young magnolia tree. Also called the leader, this branch eventually grows and is the upward extension of the tree's trunk. Do not use tree wound paint or sealants on pruning cuts. Allow the tree to compartmentalise and heal its own wounds. Do not prune in late winter since it often leads to excessive wound bleeding of sap. Also, refrain from pruning in late summer and early fall so no growth shoots appear and are later killed by frosts.