"I have a clear conscience because I know I did the right thing." We've all thought it or said it in one way or another, and it is doubtless true that doing what we believe to be the right thing helps to keep our hearts free of guilt.
However, the primary basis for a clear conscience rests not on what we do or do not do, but rather on what someone else did and does for us.
"How much more shall the blood of Christ, who through the eternal Spirit offered Himself without spot to God, purge your conscience from dead works to serve the living God?... Let us draw near with a true heart in full assurance of faith, having our hearts sprinkled from an evil conscience" (Hebrews 9:14; 10:22).
A stained conscience results in countless spiritual, moral, mental, emotional and even physical pathologies. Only the saving grace of the Lord Jesus Christ can enter into the depths of our hearts to cleanse us of the internal consequences of sin. Again, a clear conscience primarily depends on His doings rather than our own. The more we understand the Biblical revelation of our Lord's atoning work on our behalf, the more we will experience the peace of God in our hearts that assures us of full forgiveness, cleansing, and the wonder of being "accepted in the Beloved" (Ephesians 1:6).
Upon this basis of grace, we go forth to act in a manner far more conducive with a clear conscience. "We trust we have a good conscience, in all things willing to live honestly" (Hebrews 13:18). Such experience is fruit, however, and must never be confused with the root of Christ's justifying work on our behalf. Thus, our joyous declaration becomes, "I have a clear conscience because I know He did the right thing!" Our own proper doings flow from this gift of a cleansed inner temple that leads to a life reflective of the presence and work of the Lord Jesus on our behalf.
"Therefore being justified by faith, we have peace with God through our Lord Jesus Christ."