It may be a bit frightening the first time your prune your miniature citrus tree, but pruning is necessary to keep the tree healthy, to encourage it to bear fruit, and to maintain a pleasing shape. If your miniature citrus tree is keep indoors, it can be trimmed any time of year. Outdoor-grown trees should be pruned in late winter or early spring, just before the tree blooms.
Begin with sharp pruners, and clean them before you begin by wiping them with rubbing alcohol. This will prevent the possible spread of disease or bacteria.
Pinch off the tips of branches as needed to maintain the tree's compact size and attractive shape. Pruning them off as the need arises is quicker and easier than waiting until the branches are longer, thicker, and require more drastic pruning. This light pruning can be done with your fingers or with pruners at any time of the year.
Locate the graft union, which is a diagonal line or scar on the trunk a few inches above the surface of the soil. Remove any suckers, or shoots that that grow from below the line. Suckers will draw nutrition and moisture from the miniature tree, and will cause it to produce smaller, flavorless fruit. To remove suckers, pull them out with your hands, because cutting them will encourage the growth of more suckers.
Prune any dead branches and any branches that are weak or spindly, as well as any that grow inward, are crossing other branches, or are growing across the middle of the tree. This will allow more sunlight and air to reach the center of the tree.
Remove container-grown miniature citrus trees from their pots every three to four years, and trim the root system with pruners. This will control the growth of the tree, and will maintain its miniature size for many years. Trim several inches of root from the root ball, and replace the tree in the pot, using fresh potting soil.