Would your native speakers' ears feel uncomfortable and confused if I said:
"to praise in beautiful words"
"to priase using beautiful words"
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Prepositions are always difficult to learn, because their use is highly idiomatic. Although I might say "to praise in beautiful words," I would be more likely to say "to praise with beautiful words." I would be less likely to use "using" in this context.
(While I'm writing this, Choirbean has posted a similar answer.)
On the other hand, I would say that in is more common here:
He praised our work in a beautiful speech.
The idea of in here is that the praise is contained in the speech, while we are less likely to think that the praise would be contained in the words. In that case, the words would be used to praise.
But then, we have this:
One may find in beautiful words a comfort in troubled times.
Using with beautiful words here would be unusual at best, and hard to understand. Probably, in this case we think more of the emotions that the words evoke, and therefore think of those emotions as being in the words. However, that's speculative. Reasons we use one preposition over another in a given context usually are.
Would we be confused? Probably not, but it might depend on the context. That said, we might be more likely to use the preposition with, and we would usually name the object of the praise:
"Our job here is to praise God with beautiful words," said the Pastor, "not because our beautiful words move God, but because they move us."