c. 1200, "faculty of knowing what is right," originally especially to Christian ethics, later "awareness that the acts for which one feels responsible do or do not conform to one's ideal of right," later (late 14c.) more generally, "sense of fairness or justice, moral sense."
This is from Old French conscience "conscience, innermost thoughts, desires, intentions; feelings" (12c.) and directly from Latin conscientia "a joint knowledge of something, a knowing of a thing together with another person; consciousness, knowledge;" particularly, "knowledge within oneself, sense of right and wrong, a moral sense," abstract noun from conscientem (nominative consciens), present participle of conscire "be (mutually) aware; be conscious of wrong," in Late Latin "to know well," from assimilated form of com "with," or "thoroughly" (see con-) + scire "to know," probably originally "to separate one thing from another, to distinguish," related to scindere "to cut, divide," from PIE root *skei- "to cut, split" (source also of Greek skhizein "to split, rend, cleave").
The Latin word is probably a loan-translation of Greek syneidesis, literally "with-knowledge." The sense development is perhaps via "to know along with others" (what is right or wrong) to "to know right or wrong within oneself, know in one's own mind" (conscire sibi). Sometimes it was nativized in Old English/early Middle English as inwit. Russian also uses a loan-translation, so-vest, "conscience," literally "with-knowledge."