What can someone who is married to an atheist and later becomes a Christian do? What are their options?
There are hundreds of people who were former atheists who married other non-believers but then they came to saving faith in Jesus Christ. It might be within the first year of their marriage or after twenty years so, but then that joy can fade a bit when they realize that they’re married to an atheist, making them unequally yoked. And it was through no fault of their own. This is one of the hardest places in marriage that anyone can find themselves. In other cases, the engaged parties professed to be a Christian before marrying but then the Christian partner finds out later that they were lied to and they’re not really a Christian at all (1 John 3). They too find themselves in an unequally yoked  marriage, and again, through no fault of their own. What can a believing spouse do in such a marriage? Should they divorce?
Pray for Them
If Jesus tells us to pray for our enemies, do good to them that hate us, and to love those who misuse or abuse us (Matt 5), then how can we not at least do that for our unbelieving spouse? Jesus ramped up the Ten Commandments by making them internal and not just external actions of obedience. For example, Jesus said we can commit murder in our hearts if we have hatred toward anyone, including our own spouse (Matt 5:21-26), so when your spouse attacks you with wounding words, remember “Blessed are you when others revile you and persecute you and utter all kinds of evil against you falsely on my account” (Matt 5:11). Yes, words do hurt but to Jesus it doesn’t really matter. God gives us no plan B; He says “Love your enemies and pray for those who persecute you” (Matt 5:44). We should think about Jesus dying on the cross for His enemies and wicked sinners (Rom 5:8, 10), which is all of us, so I say, pray for those who hate you for we were once such as they are now (1 Cor 6:11) and were no more worthy of being saved than they are.
Pray for your unbelieving spouse that God would send them the Holy Spirit to, first of all, show them what sin is and have them recognize their sinful status before God (Isaiah 59:2). Then pray for the Spirit to convict their hearts of the need to repent (Acts 2:37-38), which means to change their mind about sin and agree with God. And finally, pray for God to have the Holy Spirit cause them to see their need for Jesus Christ, the Savior and then to bring them to saving faith in Christ by the free gift of grace (Eph 2:8-9) so that they might put their complete and uttermost trust in Christ (John 11:25-26). Please don’t make the mistake of pressuring them or preaching to them; we all make a poor imitation of the Holy Spirit. We might end up driving them further from God. Don’t get between the rock (the unsaved) and the Hammer (God). Live it, love it, and leave it; that is leave it up to the Lord because only God alone gives the increase (Acts 2:47).
The Apostle Peter’s advice for the woman married to an unbeliever is to live a submissive life “so that even if some do not obey the word, they may be won without a word by the conduct of their wives” (1 Pet 3:1) but submitting only “as unto the Lord” meaning she won’t break the law of God just to submit to her husband. Her first allegiance is to God and His Law. Peter is saying that they might “be won without a word by the conduct of their wives” and the same for men, having won their unbelieving spouse by their conduct. Paul says the same thing essentially but speaks to both men and women by his asking “For how do you know, wife, whether you will save your husband? Or how do you know, husband, whether you will save your wife” (1 Cor 7:16). This is obviously not biblical grounds for divorce . Paul says to “let each person lead the life that the Lord has assigned to him, and to which God has called him. This is my rule in all the churches” (1 Cor 6:17) and asks, “Are you bound to a wife? Do not seek to be free. Are you free from a wife? Do not seek a wife” (1 Cor 6:27). Stay where you are in other words. Pray for them and love them but make sure you know what type of love it is. Love is not just sending cards, flowers, notes, or saying it. Love is a verb and they’ll remember your actions long after your words. What you do for them is how you prove it. What you say is meaningless until something’s done to show it. Winning them “without a word…by your conduct” is possible when it is God’s will and doable by us, it is our will.
Do Good to Them
We know we should pray for our unbelieving spouse. We also know that we must love them like nobody’s business but we should also do good to them, even when they least deserve it. I remember a preacher once saying, “When your child is the most unlovable of all is precisely the moment they need to be loved the most.” Jesus tells us, “Love your enemies, do good to those who hate you, bless those who curse you, pray for those who abuse you. To one who strikes you on the cheek, offer the other also, and from one who takes away your cloak do not withhold your tunic either” (Matt 5:27-29). If you do good to your unbelieving spouse even when they don’t do good to you, then you’re following Jesus’ teachings. God will bless you for that but Jesus adds that we must bless them who curse us. If we ask God’s blessing on them, then “you will be sons (and daughters) of the Most High, for he is kind to the ungrateful and the evil” (Luke 6:35b) and He expects us to do the same!
I guess I don’t have enough faith to be an atheist because of all the external evidences of God in creation (Psalm 14:1; Rom 1) and from internal evidence in the Bible, which comes with its own exceedingly substantial archeological, historical, as well as fulfilled prophetic and manuscript evidence (numbering in the thousands). In the first place, let me ask you if you are an atheist, what evidence do you bring to me that God doesn’t exist? You might say to me, “Well, what evidence do you have that the tooth fairy doesn’t exist?” Does the tooth fairy have any genealogical evidence? Are there any secular historians who wrote about her, it, or whatever it is? Have there been any archaeological digs where artifacts or written manuscripts have been substantiated that the tooth fairy existed (like the Bible has)? My final point is that we can share our faith with an unsaved spouse and then leave it in God’s hands. We can only love them unconditionally, we can pray for them regardless of how they treat us, and we live a life above reproach, “so that even if some do not obey the word, they may be won without a word by the conduct of their wives” (or husbands) (1 Pet 3:1).
Something else that might interest you: Christian Advice Before Marriage 
Resource – Scripture quotations are from The Holy Bible, English Standard Version® (ESV®), copyright © 2001 by Crossway, a publishing ministry of Good News Publishers. Used by permission. All rights reserved.