The sentence was written in a conclusion and the topic is about simple ways to keep healthy.
"By taking it one step at a time, you'll be on your way to a more fulfilling life in no time."
Does it sound more natural to leave "it" out?
The difference is small, however I would suggest the following nuances:
Taking it one step at a time would be a reference to the general mindset of the person. For example, it would suggest making small changes, but does not preclude the possibility of taking several of the suggested measures simultaneously.
Taking one step at a time would be to adopt only one of the suggested measures at a time, and conquer it before moving on to the next. But contrary to the first, it does not suggest a laid-back mindset. The reader could be an aggressive health nutter and still fulfil this condition as long as they only looked to change one thing at a time.
Either way is fine.
The "it" seems to refer to the changes in lifestyle you need to keep healthy, which can feel radical to some.