Is your heart hurting today over trouble in your church? Do you find yourself unsure about how to even begin praying?

If you could use some inspiration for your prayers, here are three keys to praying about trouble in your church.

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Who is praying on the wall?

These keys are not intended to be an all-inclusive list, but which are a good starting point for your prayer journey when any church is hurting.

Key 1: Pray earnestly for the individuals who are hurting.

Don’t pray for the church organization first; pray for the people who are hurting first. Our call is to bear one another’s burdens and pray. And when people are hurting because of a church split, a scandal, infighting, or because of any other painful situation, we need to remember that we are all brothers and sisters in Christ. We are the family of God. And when family weeps, we all weep.

So no matter who is hurting in the church, ask God to touch them and comfort them. Ask Him to give them wisdom; to heal their hearts, bodies, and lives; and to minister to them at the point of their need.

Key 2: Pray for the people who are causing the trouble to be brought to repentance—and to justice, if needed.

It’s easy to remember to ask the Lord to help people repent. But, if laws have been broken, justice is also required.

Righteousness and justice are the foundations of God’s throne. Both righteousness and justice are required in every situation, in order for any “working through” of the process to be holy. And while we ask God to have mercy and change people’s hearts, that does not mean He shouldn’t allow them to face the consequences of what they have done. Justice must be served.

When legal issues are involved, the law must be followed. And when the Scriptures require an additional spiritual process, then the Scriptural process must be followed as well—but legal consequences must be met. Pray over these things earnestly.

Key 3: Realize that every sin grieves the heart of God. Pray earnestly in sympathy with God’s heart.

It is God’s will for His Kingdom to come, and for His will to be done on earth as it is in Heaven, in every situation. It is His will for His Body to be a pure and spotless Bride, without spot or wrinkle.

It is NOT His will for our Lord Jesus to be “crucified again” through the sins (flagrant or otherwise) of people who claim His name. According to 2 Peter 3:9: The Lord is not slack concerning His promise, as some count slackness, but is longsuffering toward us, not willing that any should perish but that all should come to repentance (2 Peter 3:9 NKJV). (Note that the key in 2 Peter 3:9 is repentance, not “restoration to ministry.”) And it is His will for us to know them by their fruit.

God, have mercy on us all.

So when we have trouble in the church, we can all practice “identificational repentance”—which means repenting on behalf of the Body of Christ at large for things we did not personally do.

In Daniel 9:3-4, Daniel practiced identificational repentance for the sins of God’s people Israel. This passage says:

Then I set my face toward the Lord God to make request by prayer and supplications, with fasting, sackcloth, and ashes. And I prayed to the Lord my God, and made confession, and said, ‘O Lord, great and awesome God, who keeps His covenant and mercy with those who love Him, and with those who keep His commandments, we have sinned and committed iniquity, we have done wickedly and rebelled, even by departing from Your precepts and Your judgments’ (Daniel 9:3-4 NKJV).

God heard Daniel’s prayers of repentance and intercession and sent mighty answers. And even though our prayers today for the Body of Christ DO NOT, in any way, negate the need for individual repentance and justice for and by those who have sinned or committed crimes, a righteous response from the Body will include corporate repentance for the fact that there is sin or division or ugliness in the Body of Christ AT ALL.

So, as our hearts break for any church that is having trouble …

As we pray for those who are hurting; as we cover any applicable legal processes in prayer; and as we pray in sympathy with the heart of God … we must also pray and ask the Lord to forgive us as a whole in the Body of Christ for the sins of the few.

We must implore Him earnestly to purge us, to correct us, and to scourge us if needed—whatever it takes to keep us on a short leash and keep sin out of our lives, both individually and corporately.

After all, Hebrews 12:6 says, For whom the Lord loves He chastens, and scourges every son whom He receives (NKJV). If praying for God’s correction and even scourging will keep us individually out of sin, should we not be praying for His corrective hand in our lives every day? Should we not continually beg Him to scourge His entire Body if necessary, in order to purify us and keep us from sinning against Him?

Of course we should.

Beloved, there is no joy in discovering that any church is having trouble.

But we, as the Body of Christ, must come together in prayer to pursue righteousness and justice (which are the foundation of God’s throne) when these things arise. We must not allow ourselves to take sides, opinions, or positions that do not align with righteousness and justice. We must only seek what the Word of God says, and pursue holiness, without which no one will see the Lord.

And all the while, we must pray AND do what we can to see those who are wounded by church issues healed and set free, and justice brought where it is needed.

Do you love the local church? Then pray this today:

“Father God, in Jesus’ name, we ask You to have mercy on all of our souls. Help us in our local church congregations:

• Help everyone in our churches to walk in holiness.
• Let every leader, every parishioner, and every sinner who walks in the doors all receive a touch from You this day.
• Reveal Jesus to us in a new and living way, and help us to give our all to Him and live for Him in a way that is obvious to every person around the world.

In Jesus’ name, amen.”

What other prayer tips can you offer to those who are praying about trouble in their local church right now? Leave your best tips below.

Jamie Rohrbaugh is the founder and CEO of From His Presence. She is the author of over 40 books, including her two latest collections of prayer tools, Wind of Heaven and New Season. She seeks to equip you to carry God’s manifest glory everywhere you go. Her resources have been published by YouVersion Bible Plans, The Elijah List, Spirit Fuel, and various other ministry outlets. Download her free prayer tool, Praying the Names of God: 555 Biblical Names of God and How to Use Them in Prayer and Worship, here. Photo credit: Photos.com/Photo Images via Canva Pro.