I Prayed have prayed
Pray: "Father God, in Jesus' name, please help each local church in America. Help us to walk in holiness, and let us dwell together in unity. Heal those who have been hurt in church, and let Your Kingdom come and Your will be done on earth as it is in Heaven."

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.

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 Godwe 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 WorshipherePhoto credit: Photos.com/Photo Images via Canva Pro.

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March 2, 2024

It is of vital importance that we, as intercessors, cover our home churches with His Word, especially those called to minister the Word of God to the people. They are under attack more than we probably understand.

We are told not to touch His anointed ones and do His prophets no harm. So, I command every evil intent meant to destroy God’s plans to be exposed and crushed by the living Word of God. I command all sexual sin to come to light and be bound from operating in our houses of worship. I declare the pulpit to be pure and holy and that those who stand as ministers of the Kingdom of God, as well as those in upfront ministry, stand blameless before the King of kings. I command angels to come into our sanctuaries to guard and protect the plans established, by God, to stand forever. And, I rebuke and bind the spirit of entertainment from being involved in our ministries, especially where it involves payment. I call in the true worshipers who can lead us to the throne room of God; who worship Him in spirit and in truth. I command all others, the wolves in sheep’s clothing, to get out and stay out. I call upon the power in the Blood of Jesus to give us undefiled worship, undefiled truth, and undefiled signs and wonders that follow the truth. I decree all ministry leaders anointed with the Holy Spirit and power and they do good and heal those oppressed of the devil. Come integrity and uprightness into our houses of prayer for you will protect us. Come holiness for you will sanctify us, and come fear of God for you will keep us by your righteous right hand. Come Guardian of our mouths in order for His Kingdom to continue advancing. Let the rivers of life be released and the trees planted by the waters heal the nations. In Jesus’ mighty name. Amen

Brian Lynch
March 2, 2024

Lord Jesus, it is my prayer that any and all hurts that have been perpetrated in the Body of Christ will be dealt with in a positive, responsible fashion. There is no place for this kind of childish, self-centered sinful behavior. As a body, we need to put aside personal differences, and become unified as a Church. Manmade divisions , like denominational pride, need to fall. None of our selfish ways of conducting ourselves were God’s ideas. Lord, may Your will prevail. By Your grace, let the church in America become what You intend for it to be in these End times. Thank You, Jesus.

Lori Meed
March 2, 2024

Wonderful, biblical, concise, and humble article Jamie! Thank you!


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