When Church Systems and Spiritual Formation Conflict

We are waist-deep in an extended exploration of what it means to become a deep disciple, someone who intends to become more like Jesus over time. A person of depth is increasingly awake and attuned to God, other people, themselves, and the world around them, including creation and culture. Ultimately, a deep disciple becomes increasingly capable of thinking, acting, relating, and loving as Jesus does, which is something our world could certainly use more of.

As we have discovered, the journey toward becoming like Jesus is usually best taken with a small group of like-hearted sojourners. Healthy formative ecosystems intentionally bring together five elements: time, habits, community, intimacy, and instruction. Jesus modeled all five abundantly in the Gospels, and we find the same basic pattern in nearly every environment where one person is intentionally formed to become more like another.

Early childhood may be the most vivid example because it is also the season when our hearts are most tender, receptive, and formative. Children are shaped through years of time, repeated habits, family and community, emotional intimacy, and ongoing instruction. No healthy parent assumes that a weekly thirty-minute lecture will form a flourishing human being.

When these five elements are absent or fragmented in our discipleship, we live in what Soil & Roots calls the Formation Gap. The Formation Gap is one of the Three Primary Problems driving the Great Omission, the modern church’s struggle to help people actually become like Jesus.

Like the Discipleship Dilemma and the Forgotten Kingdom, the Formation Gap often remains hidden because many people have never experienced another model. The lack of deep discipleship and its consequences for individuals, churches, and cultures may be one of the best-kept secrets of modern Christianity.

Church Systems and Spiritual Formation Begin With Hidden Ideas

One reason discipleship remains shallow is that modern Christian institutions often operate from powerful ideas that are rarely examined.

An idea is an assumption, conclusion, or principle in which the heart is rooted but of which we are generally unaware. Ideas are not merely doctrines or conscious beliefs. They are experienced realities that shape what feels normal, obvious, desirable, or necessary.

We all inhabit cultural ideas involving freedom, success, consent, leadership, authority, gender, government, achievement, and progress. We also carry deeply personal ideas about our identity, value, safety, power, and purpose.

Most people never intentionally examine these assumptions. We simply live within them because they feel like the air we breathe.

A person of depth, however, becomes increasingly attentive to the ideas shaping both the heart and the surrounding culture. As we explore the formative role of community, we should be willing to examine the ideas driving modern church systems and ask whether those systems are helping people become more like Jesus.

That question is not an attack on churches. It is an invitation to courageous honesty.

Are We Primarily What We Think?

One of the most powerful ideas shaping Western Christianity is that human beings are formed primarily through information.

This assumption helps explain the extraordinary emphasis placed on the sermon in many Protestant churches. We would struggle to find another formative environment—marriage, addiction recovery, military training, college, childhood, athletics, or apprenticeship—that regards a thirty-minute weekly monologue as the most formative event in a person’s life.

Yet many churches organize themselves around precisely that expectation.

The sermon becomes the centerpiece of the week, and the person delivering it may receive celebrity status. Members gather, listen, take notes, and leave, often with little expectation that they will become known, challenged, accompanied, or formed through deep relationships.

This approach reflects René Descartes’ incomplete and reductionist anthropology: we are what we think. Give people the correct ideas, and their lives will gradually follow.

Of course, instruction is essential to Christianity. Scripture, theology, teaching, correction, and wisdom matter enormously. The problem is not that we value instruction too much, but that we often expect it to accomplish what requires time, habits, community, intimacy, and embodied experience.

We have allowed many of the other formative elements to fade.

When Knowledge Matters More Than Character

The idea that we are primarily formed through thought pervades modern Christianity, and the consequences can be severe.

The accumulation of theological knowledge is often valued more highly than the kind of person someone is becoming. Biblical accuracy, verbal skill, charisma, and platform may outweigh humility, honesty, relational maturity, repentance, and compassion.

Western Christian culture continues to celebrate teachers primarily for knowledge and communication. If someone offers fresh insights with confidence, wit, and apparent authority, we may overlook—or actively defend—troubling character.

We tolerate in leaders what we would not tolerate in close friends.

We may also tolerate the same disintegration within ourselves. As long as we possess correct beliefs and can defend them, we may avoid asking whether our anger, anxiety, control, pride, resentment, and lack of empathy are actually diminishing.

The Christian life becomes an exercise in possessing the right information rather than becoming a certain kind of person.

That is a dangerous exchange.

Why Large Institutions Can Hide Character

When knowledge and charisma matter more than character, institutions can expand without requiring genuine relational access to their leaders.

We do not need to know the teacher. We simply need to hear the teaching. The larger the auditorium and audience, the more successful the ministry appears.

The leader becomes increasingly distant from the people supposedly being served. Layers of staff, boards, security, communications teams, and loyal followers protect access and shape the public narrative.

Members do not need to become vulnerable with one another either, provided they continue receiving a weekly dose of biblical information. People can disappear inside large institutions while remaining faithful attenders, donors, volunteers, and consumers.

That disappearance may not always be intentional, but it often serves the system.

People who remain unknown ask fewer disruptive questions. They are easier to mobilize, measure, and manage. They may become deeply attached to the institution without anyone becoming deeply attached to them.

Church systems and spiritual formation begin to conflict when institutional participation is mistaken for relational discipleship.

When Platforms Insulate Leaders

Several years ago, a world-famous Christian apologist died just as credible allegations began emerging regarding his abuse of women.

He had defended the Gospel before enormous audiences and built a global institution based on biblical information, apologetics, and public credibility. He continued communicating Christian truth powerfully while apparently living in direct contradiction to it.

It is difficult to believe that no one close to him suspected anything. The more difficult question is whether the institution would have responded differently if the truth had surfaced earlier.

The ministry was large, respected, financially successful, and influential. Millions of people benefited from its content.

What happens when exposing a leader threatens everything built around that leader?

In 2024, several celebrity pastors and teachers resigned or were removed after serious character failures became public. Each had built a substantial platform that insulated them from the people they were meant to serve.

More recently, a globally respected theologian died and received predictable waves of glowing tributes, even though he and his church had faced credible allegations of spiritual abuse, harassment, and gaslighting for years.

We have created a class of Christian celebrities whose influence rests more heavily on knowledge, productivity, and reputation than on being known within accountable relationships.

That class bears little resemblance to Jesus.

Institutional Success Can Silence Truth

A successful institution develops interests of its own.

Budgets need to be met, buildings maintained, staff paid, attendance preserved, donors reassured, brands protected, and programs sustained. None of these concerns is inherently corrupt. Every organization requires competent stewardship.

The danger appears when institutional survival becomes more important than truth, repentance, justice, and the actual good of people.

A leader may become too valuable to confront. A donor may become too important to offend. A scandal may become too expensive to acknowledge. A victim may be encouraged to remain silent for the sake of unity, mission, or reputation.

The institution begins protecting itself rather than seeking reality.

At that point, the system is no longer merely failing to form people. It may be actively deforming them.

Members learn that appearances matter more than truth, loyalty matters more than integrity, and institutional success can excuse relational harm.

When Spiritual Gifts Matter More Than Character

A similar problem appears in communities that prioritize spiritual gifts, supernatural experiences, prophetic claims, or emotional intensity over the slow formation of character.

I once attended the annual conference of a Christian organization where every staff member was required to meet privately with a person described as a “prophet.” Curious about the experience, I attended one of his sessions and spent the next ninety minutes increasingly disturbed.

This man, a board member and close friend of the ministry president, extracted intimate personal information from employees under the guise of spiritual discernment. The environment communicated that his access, insight, and authority came directly from God.

The entire experience reeked of manipulation, control, and spiritual abuse, which was later confirmed. Yet the practice continued.

For all practical purposes, the organization functioned like a cult wrapped in evangelical language.

The prophet’s apparent gifting protected him from normal relational scrutiny. The institution rewarded spiritual spectacle without requiring the kind of humility, consent, accountability, and character that should govern every Christian relationship.

A claimed gift became more important than the person wielding it.

Are These Merely Outliers?

Some people may argue that these examples are exceptions and that most Christian leaders sincerely desire to follow Jesus and serve people well.

I believe that is true.

Many pastors, teachers, staff members, elders, volunteers, and institutional leaders are sincere, sacrificial, faithful, and deeply loving. Churches accomplish extraordinary good through worship, teaching, care, generosity, service, community, and mission.

The point is not that institutions are inherently corrupt or that all leaders are secretly dangerous.

The concern is that certain institutional structures and incentives can quietly work against genuine formation, even when the people involved possess good intentions.

In my own experience with Western faith-based organizations, the larger the institution becomes, the greater the temptation to preserve the organization and the interests of its leaders, provided the correct version of the Gospel continues being preached.

The system begins demanding survival.

Jesus, however, invites surrender.

As Dietrich Bonhoeffer wrote, when Christ calls a person, He bids them come and die.

Systems Naturally Seek Self-Preservation

Institutions are not living beings, but they often behave like organisms intent on survival.

They develop routines, structures, incentives, hierarchies, narratives, and defenses designed to preserve stability. Over time, the preservation of the system can become confused with the preservation of the mission.

Questioning a program becomes questioning the church. Challenging a leader becomes opposing God. Naming harm becomes divisive. Leaving becomes betrayal.

People learn that belonging depends upon cooperation with the system’s preferred narrative.

This dynamic does not always result from malicious leadership. Sometimes it emerges gradually because people fear uncertainty, financial loss, conflict, or public embarrassment.

The institution’s survival becomes a hidden idea governing everyone’s behavior.

When that happens, the system may continue preaching sacrifice while demanding that others sacrifice themselves for it.

Spiritual Formation Is a Team Sport

The journey toward becoming more like Jesus is ultimately relational, not merely instructional.

That means any institution claiming to make disciples should be structured so that people can both know and be known. Being known cannot simply mean that someone records our attendance, remembers our name, tracks our giving, or notices when we volunteer.

Deep formation requires relationships in which our actual hearts become visible.

Perhaps our institutions need more dialogue and less monologue. Perhaps people need environments where they can express doubts, disagreements, fears, and questions without being interpreted as disloyal or dangerous.

If, as C. S. Lewis suggested, God often works on us through other people, then Christian institutions should make room for the kind of committed, relational communities in which that work becomes possible.

This does not mean merely expanding the modern small-group system. Small groups can be helpful, but many remain focused on content, curriculum, or church logistics rather than intentional character formation.

We may need to recover a deeper kind of community, one that brings together all five elements of formation.

What Would a Formative Church Expect?

If the purpose of life with Jesus is to be conformed to His image, then Christian communities should expect measurable changes in character, though not necessarily changes easily captured in spreadsheets.

We should expect people to become less angry and controlling, more capable of forgiving enemies, more generous with money and time, more attentive to creation, increasingly relationally shrewd, and more willing to suffer with one another.

We should expect growing freedom from anxiety, fear, manipulation, and the desperate need for approval.

We should expect leaders who become humbler as influence expands, not more insulated. We should expect communities where repentance is normal, confession is safe, and character matters more than platform.

The central question is not merely whether people know more Bible than they did five years ago.

The question is whether they love more like Jesus.

Are Our Institutions Producing This Kind of Fruit?

I am not a revolutionary, and I doubt most readers are either.

I respect Christian institutions and recognize the enormous good many of them accomplish. I do not believe the answer is to abandon every church, dismantle every structure, or pretend that small communities are automatically healthy.

Still, we should be willing to ask what our systems are actually producing.

Are people becoming less anxious, less angry, less defensive, and less controlling because of their participation?

Are marriages becoming healthier, leaders more accountable, communities more generous, and people more capable of loving those with whom they disagree?

Is intentional character formation a central purpose of the institution, or is the institution primarily organized around attendance, content, growth, giving, programming, and influence?

What does the system reward?

What does it excuse?

What does it protect?

Those answers tell us what kind of people the institution is actually forming.

Formation Cannot Be Mass-Produced

Deep spiritual formation is slow, personal, relational, and difficult to scale.

A sermon may influence thousands at once, but intimacy does not work that way. A conference can inspire a crowd, but it cannot know them. A curriculum may provide language and insight, but it cannot remain beside a person through grief, conflict, failure, and repair.

Institutions naturally prefer methods that can be repeated, measured, controlled, and expanded.

Formation often resists all four.

The deepest work of Jesus usually occurs in places that appear inefficient: long conversations, meals, friendships, prayer, shared suffering, silence, confession, repeated habits, and people remaining together over time.

These experiences cannot be mass-produced.

They can only be cultivated.

The Formation Gap Inside Institutions

This tension is part of the Formation Gap.

People may receive excellent instruction and participate in large Christian communities while lacking meaningful time, shared habits, trusted intimacy, and relationships capable of supporting deep transformation.

The institution may assume that these elements will emerge naturally, but they often do not. Busy schedules, constant programming, rotating groups, performance expectations, and fear of vulnerability can keep relationships shallow.

People remain informed but unknown.

They become involved but not necessarily integrated.

They may serve others while remaining disconnected from their own hearts.

Resolving the Formation Gap does not require destroying institutions. It requires acknowledging what institutions can and cannot do, then intentionally cultivating environments where all five formative elements can operate together.

Small Communities Are Not Automatically Safe

It is also important to avoid romanticizing small communities.

A small group can be controlling, manipulative, unhealthy, and spiritually abusive. Intimacy can be weaponized, power concentrated, and vulnerability exploited.

We recently explored how narcissism in Christian community can distort reality and damage the very people seeking formation.

The answer is not simply “small church good, large church bad.” Size is not the central issue.

The real questions involve character, power, safety, accountability, purpose, and whether the community genuinely seeks the good of its members.

A small ecosystem becomes formative when it brings together time, habits, community, intimacy, and instruction under the way of Jesus.

What Institutions Can Do Well

Healthy institutions can provide resources, teaching, worship, coordination, mission, accountability, care, and public witness. They can protect vulnerable people, train leaders, steward money responsibly, support communities, and accomplish work too large for a small group to manage.

Institutions become especially helpful when they understand that their role is not to replace relationships but to support them.

A healthy church may provide excellent teaching while helping people form smaller, long-term communities. It may distribute power, require accountability, welcome questions, and refuse to build the entire organization around one charismatic leader.

It can measure success not only through attendance and giving but through stories of reconciliation, freedom, healing, generosity, and growing character.

Church systems and spiritual formation do not have to conflict.

The conflict emerges when the system becomes the goal.

From Institution to Ecosystem

Perhaps Christian institutions can recover their most helpful role by thinking less like providers of religious goods and more like gardeners of formative ecosystems.

Gardeners do not force growth. They cultivate conditions in which life can emerge.

They tend the soil, provide water, protect against threats, prune when necessary, and remain patient with slow progress.

In the same way, healthy institutions can cultivate time, habits, community, intimacy, and instruction. They can create pathways toward being known rather than merely counted.

They can form leaders whose primary responsibility is not platform preservation but the goodness of the people entrusted to them.

They can build cultures where truth is welcomed even when it is costly.

The Courage to Ask Better Questions

It takes courage for institutions and their leaders to examine the ideas governing their systems.

What would happen if the pastor were no longer the central personality of the church? What if growth slowed because deeper relationships required more time? What if financial success did not automatically prove faithfulness?

What if people were encouraged to ask whether the institution was helping them become more like Jesus?

These questions may feel threatening because they challenge familiar measures of success.

They may also open the door to renewal.

The goal is not institutional destruction. The goal is greater alignment between the structures we build and the kind of people Jesus invites us to become.

The Invitation Beyond the System

Followers of Jesus should lead the way in addressing the loneliness, fragmentation, and relational shallowness of modern life.

That may require recreating small, trusted communities that appear unusual even to some existing Christian institutions. These communities may be slower, less efficient, more vulnerable, and less easily controlled than familiar programs.

They may also be the places where people learn to forgive enemies, relinquish control, become less anxious, suffer together, tell the truth, and experience the love of Christ beyond intellectual knowledge.

Christian institutions can support this work, but they cannot substitute for it.

The invitation is not merely to attend, consume, agree, or serve.

It is to become like Jesus together.

Duc in altum.

Explore Further

The Formation Gap

Why Information Alone Does Not Produce Spiritual Formation

How Narcissism in Christian Community Damages Spiritual Formation

Why Deep Christian Community Is So Hard to Find