The phrase that comes to my mind is, “There's more to him (or her), than meets the eye.”
One website describes this idiom to mean:
Meaning of more than meets the eye: You can say there's more to something than meets the eye if it's more complex, more important or more interesting than it seems at first.
The phrase can be applied to a situation, but, when applied to a person, it generally means that that person “has more to them” than one might initially assume, particularly when it comes to nobler qualities, such as intelligence or helpfulness. It doesn't necessarily pertain to cleverness, although it certainly can:
Ed: Mike seems rather slow sometimes.
Ted: Oh, don't underestimate Mike! There's more to him than meets the eye.