What Is the Difference Between the Holy Spirit and My Conscience?

Here’s a simple example: generations of families ran moonshine in the hills of Southeast Kentucky and Northeast Tennessee. The clear intoxicant was the source of much economical gain for these families. People from the outside and law enforcement clearly considered it wrong as many were arrested.  

However, the families who grew up on the profits did not feel the venture as violating their own consciences because of the ingrained acceptance through the years.

A Conscience Can Become Polluted

The Holy Spirit will always provide a clean conscience, but a clean conscience is not necessarily the product of the Holy Spirit. Thus, a person cannot judge his or her fellowship with Christ with the cleanliness of the conscience. 

Many liars, cheaters, and adulterers sleep quite well at night. 

Most notably the Word of God teaches that sin can lead to a condition of fleshly content. In 1 Timothy 1:5, Paul preached that faith and good conscience work hand in hand because the rejections of either “have made shipwreck of their faith.” 

Additionally, the conscience has polluting capabilities because of its flesh component. In Titus 1:15, Paul taught, “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.” Thus, the human mind and conscience is capable of being defiled. The conscience is still present, but in a state of defilement. 

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The Holy Spirit is a distinct person unlike that of the human conscience. The Holy Spirit does not evolve within the individual. It is the same today as it was when we first received salvation, and will be beyond our last day upon the Earth. 

Moreover, the Holy Spirit cannot be conditioned into subservience or acceptance of any situation contrary to its work ordained by God. 

There are distinguishing factors between the human conscience and the Holy Spirit. The conscience contemplates a self-dependence and a reliance of genetic makeup, life experiences, and influences.   

The Holy Spirit, however, is a totally different entity which is at constant battle with the flesh. Even though the Holy Spirit indwells the believer, it is a separate and distinct entity.

Only a person who has accepted Jesus Christ as Lord and Savior is indwelled of the Holy Spirit. Thus, any actions of the lost are self-dependent and self-reliant. The conscience is prone to deception. In 1 Timothy 4:2, Paul taught that “through the insincerity of liars who consciences are seared.” We are unable to give sincere reliance to the conscience. 

The believer can only boast in our “testimony of our conscience, that we behaved in the world with simplicity and godly sincerity, not by earthly wisdom but by the grace of God.” (2 Cor. 1:12)

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How does the believer know if it is the conscience or Holy Spirit directing a certain course of action? We are instructed In 1 John 4 to “not believe every spirit, but test the spirits whether they are from God.” The true Spirit of God “confesses that Jesus Christ has come in the flesh is from God.” Thus, the direction of the Holy Spirit always leads to Jesus Christ.  

If the supposed action leads to the glorification of self or the flesh, it is not of God. The conscience can deceive in this manner as its only compass for reaction and action is the present and past environment with a conditioning of mind and flesh.

But let’s go further and determine how do we know if the influence is “from God?” Paul in Galatians 5:22-23 clearly identified the fruits, or characteristics, of the Holy Spirit. Each of these “fruits” is a clear indicator when we “test the spirits.” He wrote, “the fruit of the Spirit is love, joy, peace, patience, kindness, goodness, faithfulness, gentleness, self-control, against such things there is no law.” 

Some skeptics may reply and question that the human conscience can produce these results with its action. However, the fruits of the spirit point to Jesus instead of the works by the hands of man. The conscience, on the other hand, emphasizes the abilities of man.

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The desire of the believer is “to have a clear conscience toward both God and man” as Luke spoke about this “pain” in Acts 24:16. This “pain” is not always in agreement with “man.” The conscience of the believer leads to a clear conscience by notifying man as to his sinful condition as a result of the Holy Spirit. 

Our conscience toward man can be deceived by tradition and worldly practices. Paul warned about these conditioning effects allowed by the fleshly conscience. In Colossians 2:8, we are to “see to it that no one takes you captive by philosophy and empty deceit, according to human tradition, according to the elemental spirits of the world, and not according to Christ.”  

Adrian Rodgers in his book, Kingdom Authority wrote about his visit to a local restaurant. His waitress was noticeably having a bad day. She delivered his check before her shift was to end and mistakenly overbilled him for an item, which he did not order.  

Since she had already left, he could not rectify the error in any other way. Notifying the manager could have adversely affected the employment of the waitress. The issue was magnified by the fact he only brought enough money for the meals actually ordered.  

Instead of protesting the extra charge, he instructed his wife to stay at the table while he ran home to get additional money to satisfy the bill and an appropriate gratuity. 

Conscience could have deemed correcting the bill with the manager as acceptable. The Holy Spirit, however, enabled him to realize all possible unfair results from his actions. Even though he was unfairly monetarily penalized for someone else’s mistake, no further harm resulted because of the provision of the Holy Spirit.  

The human conscience is rooted upon fairness, not divine grace and mercy. Pastor Rodgers would have been consciously justified by rectifying the error, but the Holy Spirit led in another direction. 

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In his book Of the Mortification of Sin in Believer, John Owen wrote that “in every moral action it is always either inclining to evil, or hindering from that which is good, or disframing the spirit from communion with God.” The human conscience is invariably drawn to fleshly desires and comforts. In James 1:14, we are told that “each person is tempted when he is lured and enticed by his own desire.” Thus, the conscience is closely related to the works of man which are directly opposed to the goodness of God. 

The human conscience accepts its secondary influence when in the presence of the Holy Spirit. Paul in Romans 9:1, proclaimed that, “I am speaking the truth in Christ, - I am not lying; my conscience bears me witness in the Holy Spirit.” Thus, the conscience of the believer acknowledges the power and superiority of the Holy Spirit its arrival following salvation. 

The conscience is not immune to disease. Paul warned in 1 Timothy 4:1-2 that “The Spirit clearly says that in later times some will abandon the faith and follow deceiving spirits and things taught by demons. Such teachings come through hypocritical liars, whose consciences have been seared as with a hot iron.”  

If the Holy Spirit is superior to the human conscience, how can the conscience of the believer be seared? In 1 Thessalonians 5:16, we are told to always be in a spirit of prayer and rejoicing. No matter the circumstances, the believer gives thanks for “the will of the God in Christ Jesus for you.” Further, we are told, “do not quench the Spirit.” To quench the Holy Spirit is to deny its influence.

The human conscience is judged subjectively and can be easily manipulated by “feelings” or found acceptable by the laws of a community or nation. The Holy Spirit is a separate and distinct entity in the life of the believer.

The movement of the Holy Spirit is not determined by societal norms, customs, or familial acceptance. He does not change by circumstance or societal winds of change. Often the human conscience is comforted by the fact an action or decision is supported by the laws of the land. The Holy Spirit can influence the conscious, but not vice versa, because of His independent superiority.

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