Pygmy Meyer lemon trees, also called dwarf trees, allow gardeners who don't live in a subtropical climate to enjoy their own citrus crop. Pygmy Meyer lemon trees grow in containers, and are kept outdoors during summer months and indoors during cold months. The best time to prune the pygmy Meyer lemon is late in the winter, since most fruits will have already ripened by then. Harvest any remaining fruits, then prune the tree.
Check all branches of the pygmy lemon tree, looking for damaged or dead branches. When you move your lemon tree indoors for the winter, you may damage branches by snagging the tree on a corner. Damaged branches typically display gouges or nicks. Dead branches feel hollow to the touch.
Mix a solution of one part bleach to 10 parts water, in a small container. Dip your pruners in this solution, then cut off a dead or damaged branch at the base. Dip your pruners in the bleach solution again, then make another cut. Remove all dead or damaged wood in this way. Disinfect the pruners one more time, then dry them out before moving on to healthy wood. Discard the bleach solution.
Remove suckers, which sap energy from your fruiting branches. Cut them off at the base. Suckers emerge either from the soil beside the trunk or below the graft site, which should display a faint scar.
Remove weak shoots (these will be smaller than a pencil) that are too thin to bear fruit. Trim these back to a V-intersection or to the trunk.
Thin out crowded areas of the canopy. Lemons need light and air circulation to ripen, so thinning helps promote better fruit quality. Choose weak branches and cut them off. Also remove any branches that run up against other limbs, since this causes damage to the bark.
Shape the tree. If you feel your pygmy Meyer lemon tree is too tall, clip a few inches off the top. This will promote new growth and branching. Step back and examine the tree. Make any final cuts for cosmetic reasons.