I'm looking for any manga/dj where exercise/fitness is the main theme or a big focus of the story, and they don't just mention it once.
If possible NOT a SPORTS manga, or anything like Dragonball or Dragonball Z where they train by chopping off dinosaur tailes or twitching to increase their ki. I mean something with RL training like cardio/toning/endurance exercises.

Theres holyland But thats an action manga. Its very realistic though imo.

Also, cousin its a shoujo(maybe josei I forget), about a chubby girl bou-chan who decides to work on losing weight. Its not one of those shallow "I wanna be pretty" shoujo mangas where a dork becomes a hotty by taking off her glasses and braids.

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Feed your head.

Twin Spica, maybe? Its not a main theme, but its an important role.

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although its a boxing manga you could give hajime no ippo a try. the manga revolves around a pattern of training-fight so it might be what you are looking for. gaining endurance, flexibility, reflexes, overall strength and improving specific muscle groups are all covered and built upon in the story. but as said its boxing and not bodybouilding