Elaborating on the title, I would like to read a manga with the plot having the protagonist looking weak, but actually very strong. Few examples would be something like One punch Man and Dendrobates. I also do not mind protagonists who act as if they are strong but are actually very weak, like Transfer Student Storm Bringer or Mx0

Ultimate Legend - Kang Hae Hyo kinda? He didn't "know" he was strong, so... he acted weak.

Yankee-kun to Megane-chan is the first I thought of....what else....

Black Haze
Chromed Shell Regios
Id
Trigun
Rurouni Kenshin

those are some on top of my head

also, check this out: Crouching Moron, Hidden Badass

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Angel Densetsu is a personal favorite - the protagonist looks absolutely terrifying/tough, and the intricate misunderstandings that ensue are hilarious. 😀

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Transfer Student Storm Bringer it is just excellent, i love it and couldn't stop laughing

Double Casting
https://www.mangaupdates.com/series.html?id=69432

Kuroko no Basuke I'm sure. Idk about Aoharu x Kikanjuu but the protagonist is weak-looking according to her opponents at first?

Quote from SamuraiX

Black Haze

also, check this out: Crouching Moron, Hidden Badass

THIS. This is exactly the type of progonist that you are looking for. So best advice is to check out all the manga listed there.

i just hate how i always forgets to login everytime.

Oresama Teacher, Obaka-chan, Koikatariki (alt. Obaka-chan, Koigatariki) and Gokusen sound like they might fit into this category?

Gosu (Webtoon)

I think is armin arlert (shingeki no kyojin) he look weak from the outside, but in the inside he actually clever making strategy.

[img]http://orig02.deviantart.net/38fe/f/2015/273/d/c/broken____levi_ackerman_by_absolute_emperor-d88j6ec.png[/img]

Lookism fits. The protagonist has two bodies: a short overweight body and an tall slim body, both are stronger than they look (and stronger than the protagonist knows).

This seems to be rather common in Shounen manga as well:
Gon in Hunter x Hunter, perhaps, however he only appears weak because he is a child.
Kenshin Himura in Rurouni Kenshin.

Possibly Shibatora with its baby-faced protagonist.

Not sure what genres and context you're going for but these ones maybe:

Mob Psycho 100, by the same original author who does One Punch Man, I reckon definitely fits the bill, but whether you'll like it is another matter? Art isn't great, but regardless you can enjoy it if you like the story.

Akatsuki no Yona, shoujo, fantasy, adventure. Good read if that's your thing. Heroine kinda isn't strong to start with but develops a strong mentality and will. Is training physically but wouldn't say she's amazing, but amazing from where she started from and for who she is lol.

Toukyou Kushu (Tokyo Ghoul), shounen, thriller, tragedy, mildly horror-ish, slightly gorey? You might've read it already, but protagonist trains to become gradually stronger, looks like a mild boy, but is actually very smart and tactical so he learns how to become strong quite fast (and for other reasons lol, gotta get strong asap).

Would second Ore-sama Teacher, Yankee-kun to Megane-chan for fitting the criteria, but strongly recommend oresama teacher as a hilarious read, if you can find the right scans who does good translations. Same author who did Gekkan-shoujo Nozaki-kun if you appreciate the comedy.

EDIT
Also adding in Tower of God, similar to Tokyo Ghoul where the main guy is a mild, nice protagonist but had the latent ability to become strong and does so. Story is an engaging world and adventure shounen. Would recommend!