Prune your magnolia right after it blooms. Some magnolias bloom in early spring, others in summer. Regardless of type, prune after the main flush of bloom. Some southern magnolia (Magnolia grandiflora) cultivars such as 'Little Gem' bloom all summer. Prune these early in the growing season. Late-summer, autumn, or winter pruning can result in few, if any, flowers the following year. Avoid pruning your magnolia too severely. 

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A good rule when performing major rejuvenation pruning on plants such as this is to remove no more than one-third of the plant. Pruning stresses a plant and makes it more susceptible to pests and diseases. Maintain a healthy plant during pruning by removing small amounts of growth over a period of several years.