late 14c., prouynen, proinen, of a bird, "to trim the feathers with the beak;" of a person, "to dress or groom oneself carefully," from an extended or transferred sense of Old French proignier, poroindre "cut back (vines), prune" (Modern French provigner), a word of unknown origin. Compare preen, which seems to be a variant of this word that kept the original senses.
The main modern sense of "lop superfluous twigs or branches from" is from 1540s, perhaps a separate borrowing of the French word. It is earlier in English in a general sense of "lop off as superfluous or injurious" (early 15c.).
Perhaps [Watkins] from Gallo-Roman *pro-retundiare "cut in a rounded shape in front," from pro "forth" (see pro-) + *retundiare "round off," from Latin rotundus (see round (adj.)). Klein suggests the Old French word is from provain "layer of a vine," from Latin propago (see prop (n.1)).
Related: Pruned; pruning. Pruning hook, knife with a hooked blade used for pruning plants, is from 1610s; pruning knife, knife with a curved blade, is from 1580s.