The best time to prune your lemon trees is directly related to the climate and temperature of your location. If you live in a very hot climate, such as the Arizona desert, then prune between February and April. Pruning where temperatures are more moderate should be done in late February or March.
Prune the trees before they bloom because they will lose fewer fruits. Pruning during spring allows the trees to generate foliage that will shade new branches within the canopy before the tree is subjected to summer sunlight.