The preposition by has a specific meaning with time expressions:
6. Not later than: by 5:30 pm.
If you use it, then the time expression used has to be specific, not vague or indeterminate like soon.
I will be there by ten o'clock.
I will be there by the time you are ready to leave.
I will be there by Friday.
Just ask yourself if the time expression being used works with the preposition:
I will be there not later than soon. (?)
This is grammatically possible, of course, and could be used in a flippant remark, but for most usages it would just sound odd or foreign.