“keeping your faith [leaning completely on God with absolute trust and confidence in His guidance] and having a good conscience; for some [people] have rejected [their moral compass] and have made a shipwreck of their faith.”

1 Timothy 1:19 AMP

A good conscience is a biblical conscience – and the only way to have that is through absolute trust in God.  It’s to this that Proverbs speaks when it says we shouldn’t lean on our own understanding but in all our ways and thinking consider Him as preeminent.  Yes, lean on and acknowledge Him.  One’s conscience is the God-given internal moral compass that’s either corrupted by sin’s deceit or pointed at Christ.  The Bible speaks of four different levels of conscience – seared, accusing, awakened, and good.  Let’s look at them.  

Conscience is our knowledge of good and evil.  When Adam fell it was because he decided to take of the fruit of the forbidden tree – to be like God and judge good and evil on his own terms.  In other words, Adam’s sin, as well as our central challenge to God, is to reject Him as the ultimate standard.  This rejection is a package-deal.  We reject His interpretation of life and insist on our own.  To this end, man has a moral problem that spills out into every other area.  In a very simple way of looking at life we can say that unregenerate man disagrees with God and the redeemed man agrees with Him.  The former self, with the mind set on autonomy (the flesh) sees itself as the final reference point.  The regenerate mind (walking in the Spirit) seeks His law and will over that of fallen self.  

Paul speaks of the seared conscience in chapter 4.  He says:

“But the [Holy] Spirit explicitly and unmistakably declares that in later times some will turn away from the faith, paying attention instead to deceitful and seductive spirits and doctrines of demons, [misled] by the hypocrisy of liars whose consciences are seared as with a branding iron [leaving them incapable of ethical functioning],”  1 Timothy 4:1-2 AMP

Again in Titus: 

“To the pure, all things are pure, but to the defiled and unbelieving, nothing is pure; but both their minds and their consciences are defiled.” Titus 1:15 ESV

The person with a seared conscience has no consideration whatsoever for right and wrong.  Raw power is the only thing.  The criminal, the bully, the tyrant.  

The thing is, in this state it still functions but we have an issue of profound malfunction.  It still functions but only in unabashed error.  God’s law is still written into the fabric of life and on our hearts.  No one ever forgets God’s law totally.  All people have a clear knowledge of God (Romans 1:18-21) and this includes His moral law.  One thing I’ve noticed over the years is that even the most hardened criminal is compelled to justify his crimes.  In their minds, somewhere, somehow, they’re always the victim!  

This means that even at our worst, our conscience is still revelatory of God because we must and will – absolutely – categorize all things as right and wrong.  John Frame says that in this way the conscience is, like nature, a kind of natural revelation of God.  The worst sinner still cloaks depravity in the fine coat of moral approbation.  The homosexual movement justifies what God condemns (Romans 1:26-27) and calls it good and loving.  The unspoken assumption at the bottom of it is the insistence moral righteousness.   

Next, we notice that despite our dismissal of God and His moral law-word, we’re obsessed with right and wrong.  We have very active consciences.  The problem is, outside of grace, they’re set on accusing.  

A hallmark of fallen man is his/her incessant need to simultaneously accuse others and excuse self.   Listen to the conversation of anyone long enough and you’re going to hear a moral evaluation of others – in the negative.  It’s inevitable.  Because we’re made in God’s image and can’t escape His fingerprint, and the whole world is His too, we live and move and think in a moral world as moral beings.  Therefore, we’re busy (Romans 2:14-15) either accusing or excusing.  And the foundation of the accusing conscience is its obsession with what’s wrong with others.  

If we look at something as large as politics we see the pattern all over the place.  Whole movements are animated and fueled as a means to get even with others under the guise of justice.  Modern crusades for “rights” are nothing more than bullying attempts to force people to agree rather than true equality before the law.  The modern left, as a false religion, busies itself with what’s wrong with the world and a yearning to be free of so-called systemic sins.  The sin is out there, as Albert Mohler puts it, and the solution is government.  

If you look at the individual you see the pattern in the obsession with what’s wrong with the people or organizations around them.  The compass of their heart points routinely at the sins of others, at what is owed to them, at how things aren’t their fault.  The accusing conscience has a black belt in detecting how life is unfair and what’s wrong with everyone else.  It’s a master defense witness of self and brutal prosecuting attorney of others.  

The seared conscience is the last stop of the train on the track of rebellion.  It’s where we get to the point where we’re so corrupted that we call evil good and good evil.  It’s a point where our moral confusion is so profound that we “shout our abortion” or call sexual purity evil (or intolerant or whatever).  It’s the point where we’ve gone so long resisting the word of God and His grace that we engage in full intellectual warfare against His moral order.  The seared conscience openly rejects any claim of God upon our lives and the world at large.  It flies that flag of self over all things; all things are for the self and self is all things.  It’s the culmination of pride and the result of God giving us over to the lusts of the flesh and futility of our minds (Romans 1:21).  

Next we have the awakened conscience.  Frame writes:

“But when our accusing conscience turns its guns back on ourselves, something wonderful may await us.  I say “may await us” because this wonderful outcome is not immediate or inevitable.  When their conscience breaks through their self-defensiveness, many respond by becoming all the more angry, vengeful or bitter.  Even when they come to acknowledge their own wickedness, their response is often to become miserable.  They wallow in grief, and they sense no way to unload their burden of guilt.”  

But sometimes, gloriously, God intervenes.  Our command is not to save the lost.  We must not miss the most critical distinction of Christian work lest we become discouraged.  We are called to witness, to preach, to teach, to pray.  In apologetics and in evangelism, the measure of success is Biblical faithfulness, not conversion since it is God who saves.  It’s not our own doing – either our salvation nor that of others.  When God’s love is poured into our hearts it’s like being created all over again.  Yes, we’re a new creation (2 Corinthians 5:17).  

At this point, the new man has a new conscience.  No longer is it a tool for our mere self-justification and the incessant damnation and judgment of others.   Indeed the blood of Christ purifies our conscience from its dead works – and its deadly work – to serve the living God (Hebrews 9:4).  

This begins the training of Christian life of Romans 12:1-2 and Hebrews 5:14.  Our conscience needs to be nourished by the solid food of Scripture.  

We must also understand the passages of Romans 14 and 1 Corinthians 8:7-12 where Paul speaks of “weak” consciences.  What does he mean?  Sometimes it means that someone is lazy and they let themselves off the hook.  But in these passages they’re actually too strict – forbidding what God permits.  Thus, we must be in training, like athletes, to be neither too strict nor lackadaisical.  

The “good” conscience, John Frame says, evaluates our conduct properly, as God does.  Paul says:

“This is our [reason for] proud confidence: our conscience testifies that we have conducted ourselves in the world [in general], and especially toward you, with pure motives and godly sincerity, not in human wisdom, but in the grace of God [that is, His gracious lovingkindness that leads people to Christ and spiritual maturity].” 2 Corinthians 1:12 AMP

This isn’t to say something heretical.  Namely, that we’re sinless.  That would be in clear violation of Scripture (1 John 1:8, 10).  The point of the good conscience is that the Christian won’t be guilty of the charge of fraudulent religiosity.  Perfection in this lifetime isn’t in view, Biblical faithfulness and consistency is.  The great thing to note is how the good conscience is a gift of God, showing that our actions and direction in life please Him and it reveals His character by showing what He’s done within us through grace.  

The good conscience isn’t an inoculation against the slander of unbelievers unfortunately.  Paul had plenty of detractors, for example.  But Peter said, 

“And see to it that your conscience is entirely clear, so that every time you are slandered or falsely accused, those who attack or disparage your good behavior in Christ will be shamed [by their own words].” 1 Peter 3:16 AMP

For more examples of this see Romans 9:1, 13:5, or 2 Corinthians 4:2.  Read also, Acts 23:1 and 24:16.  In fact, Paul started this very letter this way:

“But the goal of our instruction is love [which springs] from a pure heart and a good conscience and a sincere faith.” 1 Timothy 1:5 AMP