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What Are the Serious Problems That Exist in Denominations and Churches Today?

4 min read

Question by Jordan D from London.


“The true Church is not a denomination, it is a spiritual house built by the Spirit.”

Thank you, Jordan from London, for this very timely and important question. You’re not alone in asking it. Many sincere believers are becoming increasingly aware that something is deeply amiss in the visible Church. Let’s take time to answer this carefully, scripturally, and spiritually—not with bitterness or blame, but with love and clarity, for the sake of Christ’s Body.

What Are the Serious Problems That Exist in Denominations and Churches Today? #

The Bible prophesied that “judgment must begin at the house of God” (1 Peter 4:17 AMP). The Holy Spirit is now shining His light on the systems of religion and exposing the inward corruption, not to condemn, but to call out a remnant into Christ’s fullness. Let’s look at the core issues under these key categories:

System Over Spirit #

SymptomScriptureImplication
Heavy institutional structure2 Timothy 3:5 (AMP)“Holding to a form of [outward] godliness (religion), although they have denied its power [for their conduct nullifies their claim of faith].”Many churches have become mechanical and program-driven, replacing the leading of the Holy Spirit with traditions, timetables, and rituals.
Church governance like corporationsIsaiah 1:13-15 (AMP)“Bring your worthless offerings no longer… even though you offer many prayers, I will not be listening.”The business-like structure often quenches the Spirit and prevents the organic growth of the Body of Christ.

Man-Centred Leadership and Celebrity Culture #

SymptomScriptureImplication
Elevation of men above ChristThe focus has shifted from Christ being lifted to charismatic speakers, brand identity, and performance.Denominations and ministries often centre around personalities rather than Christ. Loyalty is to a pastor, bishop, or prophet, rather than to Jesus.
Platforms more than altarsJohn 12:32 (AMP)“And I, if I am lifted up from the earth, will draw all people to Myself.”The focus has shifted from Christ being lifted up to charismatic speakers, brand identity, and performance.

Commercialisation of the Gospel #

SymptomScriptureImplication
Prosperity emphasis & money schemes2 Peter 2:3 (AMP)“In their greed they will exploit you with false arguments and twisted doctrine.”Many are being led into materialism rather than spiritual growth. The focus is on sowing to get money rather than to grow in grace.
Selling “anointing” & miraclesMatthew 10:8 (AMP)“Freely you have received, freely give.”Manipulating people for money under the guise of “faith giving” corrupts the purity of the Gospel.

Division, Denominationalism, and Sectarianism #

SymptomScriptureImplication
Splits and rivalry between churchesJohn 17:21 (AMP)“That they all may be one [just] as You, Father, are in Me and I in You.”Denominations were never Christ’s idea. They are divisions in the Body, based on doctrines, preferences, and human pride.
Each claiming “we are right”1 Corinthians 1:13 (AMP)“Has Christ been divided [into different parts]?”Sectarianism blinds believers from recognising the whole Body of Christ.

Stagnant Teachings & No Spiritual Growth #

SymptomScriptureImplication
Milk-level messages with no maturityHebrews 5:12-14 (AMP)“By this time you ought to be teachers… you need milk, not solid food.”Believers remain spiritually immature because the churches fear going deep. The deeper truths of Sonship, spiritual formation, and the Kingdom are ignored.
Avoidance of hard truths2 Timothy 4:3 (AMP)“They will accumulate for themselves [many] teachers [one after another], to satisfy their own desires and to support the errors they hold.”The pulpit is shaped more by what the people want than by what the Spirit is saying.

Tolerance of Sin and Lack of Holiness #

SymptomScriptureImplication
Grace was used as a licenseJude 1:4 (AMP)“They turn the grace of our God into lawlessness and deny our only Master and Lord.”Many no longer call people to repentance. Grace is preached without the cross, the blood, or sanctification.
No dealing with flesh and Adamic natureGalatians 5:24 (AMP)“Those who belong to Christ Jesus have crucified the flesh.”Grace was used as licence

Lack of True Presence and Power of God #

SymptomScriptureImplication
Emotionalism instead of encounter2 Corinthians 3:17 (AMP)“Where the Spirit of the Lord is, there is liberty.”Many gatherings are soulish, not spiritual—entertainment over encounter, feelings over faith.
Gifts without fruitMatthew 7:22-23 (AMP)“Did we not prophesy in Your name…? But I will say to them… I never knew you.”Power without intimacy is dangerous. The Spirit is grieved when the focus is on performance, not communion.

The Root of It All #

The root issue is not denominations themselves, but that the Church has lost the centrality of Christ and the operation of the Spirit. It has become a mixture of flesh, ambition, and religion. The true Church is not in buildings or brands but in living stones being built together into a spiritual house (1 Peter 2:5).

“When Christ is no longer central, even a ‘church’ becomes a religious shell.”

“Unless the Lord builds the house, they labour in vain who build it.”
Psalm 127:1 AMP

The Call Back to Christ #

The Spirit is calling a remnant out of mixture to walk in the purity, power, and Person of Christ. This doesn’t mean rejecting all gatherings or leaders but discerning the true voice of the Shepherd and following Him. Apostolic alignment, spiritual maturity, intimacy with God, and the operation of the Kingdom are being restored, but outside of many traditional structures.

And all this is only when Christ is in you, when you are moved by the Holy Spirit, when you are dead to the world, dead to Adam and the flesh, but alive in Christ and the Spirit. Without this inner transformation, we may merely shift from one form to another.

Summary #

Problem AreaRoot IssueWhat God Desires
System-driven religionMan’s order over SpiritSpirit-led organic Body
Celebrity ministryMan-centrednessChrist alone exalted
Prosperity misuseGreed and manipulationGenerosity in love and truth
Denominations and divisionsSectarianismOneness in Christ
Shallow teachingFear of offenceMaturity and truth
Tolerance of sinCarnalityHoliness and cross
PowerlessnessAbsence of presenceCommunion with God

“Hope this helps, Jordan—and to all who are sensing these things in your spirit. The Spirit is calling us to come out of Babylon and follow the Lamb wherever He goes.” Let him who has ears hear what the Spirit is saying to the churches.

In Christ,
Shaliach.

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