By making them flawed and put more thought and focus on those opposed to their strength.
None of my current stuff features "God-like" characters, but a private piece I made with an ex friend did. I feel I illustrate points better with examples so please, humour this:
A God with the power to make everything around him rot was but a child seeking a father figure, he latched onto the high priest of his church. This of course led to his downfall as he could not bring himself to kill this priest... even though this priest was frankly the only thing that could stop him. This isn't to even mention the arrogance baked into his personality-- how could he not be? He was a god. So sure his plans and schemes were unstoppable he didn't see that a mortal sat across from him at that chess board. He couldnt see he was being set up to lose simply because the mortal was allowing pieces to get taken. No one truly could stop him, he was so sure... until his emotions got involved and a being so weak he could not even walk for lengths of time outplayed him and used his priest against him, at least.
Basically, make them human. Sheer strength is one thing, but emotions and attachments are fragile, fickle things. Being unstoppable at one thing is all well and good, even being an expert at others is fine, but don't be afraid to make them weaker than other characters in different regards. The god of my story could have just rotted away everyone, but he didnt see the sickly mortal as a threat. He didn't have the heart to kill someone he grew attached to. He wasn't perfect, even if he could technically best all these other characters.
In the same story we had a handful of characters near-god like and most of them destroyed their lives in one way or another because of it. One accidently tore a limb from her body and blinded herself in one eye because she lost control when she lost her temper. This temper and will to fight gets all the mortals she grows close to killed because they cant handle the situations she gets them into. Another plunged a whole mountainside into an eternal winter and lived in a world of ice statues of the people she once loved, ever stirred on by her depression. Frankly, she wants nothing more than to die and would welcome it. Another did not let her power ruin her, but her unflinching loyalty to her brother did. He told her to wait for him and she became a hermit in the woods who had gone mad. Any utterance of word from her brother would make her fall into line with whatever the speaker wants.
All these characters couldn't be bested by anyone but Gods if we just look at their strength or "power level" alone. But surely you can see that isn't the most important part about them. Their flaws are. Their flaws drive their stories.
Perfect characters in fiction are boring. In other words, the fact you have put this flaw into your character is a very good thing. Now don't be afraid to let it destroy her. Not killing her, if that's not the goal here. But let it ruin her life, paint her in a bad light, cause huge issues for her to navigate. Let her lose big things because of it, let her claw her way back from the destruction it leaves with skills and traits beyong her strength. Let the whole process hurt her. If your story is lighter in tone than mine, that's fine. The stakes don't have to be that high, but let the character stir up their own conflicts. Don't let their power be an "easy fix" the issues caused by their flaws as soon as they arise. Let her temper ruin things and leave her a sniveling mess with her pride cast away just begging anyone to help. Let her fight her inner frigid demons when she is given something/one to fight for. Let her see her desires take president over what others want for her and finally grow into more than a pawn. Let him taste betrayal and not have the heart to do anything about it. Focus on things that aren't just power, focus on what makes a character human.
