Let your conscience be your guide. This bit of folk wisdom seems to make sense since our conscience is designed to help us discern right from wrong. However, people cannot always trust their internal radar to steer them correctly; this is the case particularly with unbelievers, who don’t have the Holy Spirit to reveal truth and offer guidance for wise decisions. And while Christians do have God’s indwelling Spirit, they should be careful not to harbor sin in their lives, as that can interfere with the way their morality sensor functions. “Create in me a clean heart, O God, and renew a steadfast spirit within me.” (Psalm 51:10)
A trustworthy conscience is programmed with scriptural teaching. Believers build a stable and sensitive spiritual radar system by applying God’s truth to their lives. They are committed to thinking and acting in ways that honor and please the Lord. Then, when sinful thoughts or choices come across that radar, it will deliver a sharp warning.
A person with a reliable conscience will have a strong desire to obey God. He won’t settle for what feels right or looks good, but instead prayerfully seeks the Lord’s will. In other words, he does not rely solely on his conscience but incorporates all of the Holy Spirit’s tools into his daily life: Scripture, prayer, etc. Moreover, when his spiritual radar sounds the alarm, he is quick to draw back and reject unwise choices. “But the goal of our instruction is love from a pure heart and a good conscience and a sincere faith. For some men, straying from these things, have turned aside to fruitless discussion, wanting to be teachers of the Law, even though they do not understand either what they are saying or the matters about which they make confident assertions.” (1 Timothy 1:5-7)
A conscience isn’t designed to be our guide; it is a tool of the Guide. The Holy Spirit not only convicts us of sin, but He also brings to mind godly principles and leads us on a righteous path. He uses a variety of tools to conform us to the likeness of Christ (Rom. 8:29).
Source: Can You Trust Your Conscience?