Certified GKH Gardening Expert
I would hold off on pruning just yet, especially if it's outdoors. Pruning lemon trees isn’t generally required, but there are several good reasons to do so. Pruning helps improve airflow, reduce disease, strengthen limbs and makes it easier to harvest fruits. The best time to prune is early spring or late summer or anytime prior to blooming. Prune every year or two, which will help keep them from becoming too large. If you have frost damage, wait until the trees have shown new growth. Prior to pruning trees, pick off any remaining fruit. Prune all dead, damaged, weak or diseased branches to the base. Weak stems cannot withstand the weight of heavy fruit production.
Lemons require little pruning beyond cutting out damaged or dead branches, or opening up the interior so light and air get to all the greenery. These are not the kind of plant you cut back for the winter. Here's some more information on growing lemons: https://www.gardeningknowhow.com/edible/fruits/lemons/how-to-grow-a-lemon-tree.htm