it's only a matter of time건 is a contraction of 것은, meaning “as for the fact that...” or “as for ...”. This expression indicates that something is certain to happen eventually. The wording is often casual and may sound threatening depending on context.
KO: 그가 진실을 알게 되는 건 시간문제야.
EN: It's only a matter of time before he finds out the truth.