Both are different words: one is a preposition, while the other is a pronoun. Looking at the definition of en, you’ll notice two tabs: EN¹, prép. (preposition) and EN², pron. atone de la 3e pers. (3rd person pronoun).

Only the preposition can adequately be translated by “in”; you should be able to infer easily from the context whether it’s a preposition or not.

“En” can have different functions:

adverbe: indicates the origine

Il en vient / He comes from there

préposition: indicates a location, a situation, a form, a transformation, a duration, a mean

J’y vais en train / I go by train

Or it can be a gérondif, placed before a verbe : en mangeant, en jouant.

Il buvait sa bière tout en jouant du piano / He was drinking his beer while playing piano.

pronom personnel: De ce, de cela, de lui, d’elle, d’eux, d’elles

Tu n’en sais rien / You know nothing about it