You don't refer to any of the specific doctrines about this, of which there are many. So I shall just mention two different possible views.
Your question "when the soul is with the body" suggests to me a dualistic view of soul and body. But Descartes (in Meditations VI) argues that "with" or "in" is mistaken. He says:-
Now there is nothing that this my Nature teaches me more expresly then that I have a Body, Which is not Well when I feel Pain, that this Body wants Meat or Drink When I am Hungry or Dry, &c. And therefore I ought not to Doubt but that these things are True. And by this sense of Pain, Hunger, Thirst, &c. My Nature tells me that I am not in my Body, as a Mariner is in his Ship, but that I am most nighly conjoyn’d thereto, and as it were Blended therewith; so that I with It make up one thing; For Otherwise, when the Body were hurt, I, who am only a Thinking Thing, should not therefore feel Pain, but should only perceive the Hurt with the Eye of my Understanding (as a Mariner perceives by his sight whatever is broken in his Ship) and when the Body wants either Meat or Drink, I should only Understand this want, but should not have the Confused sense of Hunger or Thirst; I call them Confused, for certainly the Sense of Thirst, Hunger, Pain, &c. are only Confused Modes or Manners of Thought arising from the Union and (as it were) mixture of the Mind and Body. pg 97 in my antique edition, acquired from Gutenberg Press
A dualist has to believe that the soul controls the body, but that's not the same as changing it. I would suggest, though, that for any dualistic view, since the soul is a distinct substance from the body, they are what they are independently of each other. They do not change each other, and if/when they separate, each leaves the other as it found it. So no change.
Aristotle's hylopmorphism Wikipedia - Hylomorphism is the first version in a very long tradition and is more complicated. I'm not competent to engage in a detailed scholarly discussion. On his idea of perfection, @Mauro Allegranza provides a link to Wikipedia in his comment above. It includes the following:-
The natural end of the organism (and the means to this end) is good for it, and what defeats or impedes this end is bad. For example, he argues that animals sleep in order to preserve themselves, because “nature operates for the sake of an end, and this is a good,” and sleeping is necessary and beneficial for entities which cannot move continuously (De Somno 2.455b17–22). For human beings the ultimate good or happiness (eudaimonia) consists in perfection, the full attainment of their natural function, which Aristotle analyzes as the activity of the soul according to reason (or not without reason), i.e., activity in accordance with the most perfect virtue or excellence (EN I.7.1098a7–17). Wikipedia - Aristotle's Politics
The complication here is that the perfection of the human being is not necessarily the perfection of the body and the question of the perfection of the body without a soul (i.e. without its animating principle) is positively bewildering, because it isn't clear what its function is.
Going back to first principles, the concept of matter provides a substrate which remains the same when it acquires different forms. The classic Aristotelian example is the bronze that makes up a statue, but can be melted down and re-cast as all sorts of other things. But we can observe that a given lump of bronze, wood, or stone may have properties that make it more or less suitable to various uses. Bronze may be more or less suitable than wood or stone for making a specific statue. But that only means that its perfection is only in relation to a specific use.
But soul itself does not cause those perfections or imperfections. They are merely physical - there whether or not the soul is there. So I conclude that the answer to your question is, again, no.
There's nothing conclusive here, but it may be helpful.