It's simple.
Change the challenges they face into something their OP abilities can't necessarily solve.
Alternatively, put them up against their foil. An antagonist who's abilities are the protagonist's inverse, or one who has counters to what the protagonist can do (if you're looking for more of a battle-scenario).
As an expansion on what I said here, I'll use
Aethara: The King's Path as a point of reference.
Marius, the protagonist, is explicitly defined as being "As powerful as he needs to be" for the story; because the tension, and conflict, for his character arc is primarily moral, ethical, and internal.
The arc isn't about whether he's powerful enough to do something. It's about whether he
should do it, and
why he does it; as well as the consequences of his actions, or inactions, as the case may be.
So, Marius is by definition, an OP Protagonist, who is kept well under control through his story arc, and (in the early chapters) by discovering/remembering the abilities he has at his disposal. (All of which are part of the world's LitRPG system, and not exclusive to him as a character). This element, though, is there to assist in maintaining tension during the conflicts he faces over the course of the story.
In my (humble) opinion, there is a right way to write OP protagonists, and a wrong one, and that method ultimately comes down to the heart of their conflicts, tension, and character arc.
The ideal approach would be determined by the narrative stakes and style you're going for in your story. If you want more of a Shounen style; pitting the protagonist against their foil/inverse is usually the best approach.
For a darker story; Corruption, Morality, and Ethics should be prioritized over the character's powers or abilities; and this can be strengthened through the consequences of the OP character's actions, or lack there-of.
I do, genuinely, hope this helps any fellow authors and aspiring authors deal with the issue of OP protagonists in your stories.
Beyond this, however, it really depends on your definition of an "OP" protagonist or character.