First of all, it is easy to show that doing what our conscience allows is not always right, since there is such a thing as “sin through ignorance” (Lev 4:2, 13; 5:15, 18, etc). Moses instructed the people of old: “If any soul sin through ignorance, then he shall bring a she goat of the first year for a sin offering” (Num 15:27). Our conscience can only be a reliable guide if our knowledge of God’s commandments (cf. Lev 4:2) is adequate. Thus a professing believer who does not keep the Sabbath because of ignorance, is nevertheless sinning against the Lord. Indeed, I believe that most professing Christians are sincere. But the broad road to damnation is paved with sincerity, for our Lord tells us that at the Last Day many who call Him “Lord, Lord” will be disowned by Him because they walk in lawlessness or not in accordance to His commandments (Mt 7:23). 

Secondly, the apostle Paul teaches us in the context of his discussion on matters of indifference that “whatsoever is not of faith is sin” (Rom 14:23). What he is saying is that even though there is nothing wrong with eating meat, yet if the conscience of a professing believer forbids him to eat meat then it would be sin for him to eat meat before his conscience is properly instructed. 

But what if it is something commanded by the Word of God and not just a matter of indifference? Would a man still sin if he does what is commanded though his conscience forbids him (because he is convinced that it is wrong)? Well, I believe it is still wrong for him. Consider for example, a religious unbeliever man. He believes that it is wrong to pray in the name of Jesus, but he comes to church, and someone not knowing that he is a unbeliever asks him to pray. He prays, and ends his prayer with “In Jesus Name.” What would you call such an act? Or think of a professing believer who strongly believes that it is wrong for New Testament saints to give tithes, but yet, when the ‘offering bag’ marked as ‘tithes’ comes around, he puts his tithes in so that he does not look bad. What would you call such a person? Yes, it is hypocrisy, isn’t it? And do you realise how the Lord Jesus reserved His harshest criticism for those who act in hypocrisy? Is it not better to obey the conscience rather than sin the sin of hypocrisy? 

So the bottom line is: Let’s obey our conscience at all times. But let us make sure we do not starve our conscience by failing to instruct our minds in the truth.