When Formation Meets Doctrine
A Reflection on Penal Substitution vs. John Mark Comer’s Practicing the Way
Introduction: A Shepherd’s Heart for Formation and Doctrine
I write to those who have been deeply encouraged by John Mark Comer’s Practicing the Way, drawn to its invitation to “be with Jesus, become like Jesus, and do as he did.”1 That invitation—a posture of apprenticeship in Christ’s footsteps—speaks powerfully to generations burdened by spiritual fatigue and a Christianity reduced to script or routine. Yet, as someone who cherishes both the beauty of formation and the truths of theology, I sense a disquiet: the gospel’s heart—the reality that Christ stood in our place under divine justice—appears to be fading from the picture. When the cross is turned primarily into a lifestyle guide rather than the means by which our sins are paid for, we risk holding vibrant practices built on a shaky foundation.
I recognize the value in Comer’s aims: he gently pushes us toward embodied discipleship, stepping beyond cultural Christianity into lives shaped by spiritual rhythms. He helps readers visualize what following Jesus might look like in space, time, and relationship, especially for those disillusioned with performance-based faith. Yet, for all its pastoral warmth, Practicing the Way seldom dwells on why we follow Jesus—namely, that he absorbed the penalty our sins deserved—leaving vital gospel clarity underarticulated.2 This omission in theological substance can subtly reshape the direction of discipleship from grounded in the gospel to drifting toward mere imitation.
For the journey to truly reflect life in Jesus, we need both the what and the why—living patterns formed by grace and practices rooted in the gospel’s truth. My intention here is not to dismiss the rhythms that have renewed many weary souls but to re-anchor them in the penal substitutionary atonement: the doctrine that ensures the “why” of our faith is not an afterthought. May this reflection help those inspired by Comer to press deeper—not only how we walk with Jesus, but to the secure foundation of his once-for-all atoning work.
Understanding PSA: Why It Matters
At its heart, Penal Substitutionary Atonement (PSA) teaches that Jesus took on the punishment we deserved, satisfying the demands of divine justice so we might be forgiven and restored. The term “penal” refers to the penalty due to our sins, and “substitution” means Jesus stood in our place to bear it.3 This isn’t cold legal vocabulary; it reflects the living truth that through Christ’s atoning work, the wrath of God—our deserved judgment—was exhausted on him.4 Instead of condemnation, we receive grace. This is the jewel at the center of the gospel: not simply living well, but being forgiven—and made right—because Jesus endured our penalty.
Why does this matter for you, regardless of theological background? Simply put, PSA preserves the holy integrity of God while showcasing his boundless mercy. If sin is real—and Scripture is clear that it is—then the justice of God cannot be compromised (Rom. 3:25–26). The cross isn’t an easy escape hatch; it’s the substitutionary sacrifice by which God remained just and justifier.5 Without this truth, forgiveness risks becoming cheapened. But when you see Christ voluntarily paying what you owed, grace glows in full brilliance, not in dim imitation.
Moreover, PSA gives power to our spiritual formation. When we “practice the way” of Jesus, our obedience flows not from duty, but from gratitude to the one who already loved enough to die in our place (2 Cor. 5:21). The knowledge that Christ bore our punishment—so we might stand forgiven—transforms faith from moral striving into heartfelt response. It frees us to follow, not to earn favor, but because we already have it. In this way, PSA becomes the secure anchor for genuine transformation—not only how we walk with him, but why we walk.
What Practicing the Way Gets Right
It’s important to begin with gratitude. John Mark Comer has offered the church a fresh vocabulary for discipleship, especially for those who have felt stuck in nominal or performative Christianity. His emphasis on apprenticeship—being with Jesus, becoming like Jesus, and doing what Jesus did—feels both biblical and compelling.6 In a cultural moment of distraction and fragmentation, his call to rhythms of rest, prayer, and presence with God is a much-needed corrective. Many readers testify that his framework breathed life into their walk with Christ in ways they hadn’t experienced before. To dismiss this outright would be to ignore the genuine spiritual good many have received.
The strength of Practicing the Way lies in its accessibility. Comer writes in a voice that resonates with millennials and Gen Z—clear, honest, and relatable. He helps readers see that discipleship isn’t abstract or confined to a Sunday gathering but rather embodied in the everyday. He paints a picture of Jesus not just as Savior but as Teacher whose life is worthy of imitation. For people exhausted by shallow church experiences, Comer provides a vision that feels doable, tangible, and authentic. In this, his ministry has helped many rediscover that following Jesus involves more than intellectual assent.
Yet, while Practicing the Way shines in describing how to walk with Jesus, it often gives little attention to why we walk with him in the first place. Spiritual practices, as good as they are, cannot stand alone. Without the foundation of Christ’s saving work—his substitutionary death in our place—they risk becoming mere self-help with a Christian gloss.7 The danger is subtle: people can begin imitating the practices of Jesus without truly understanding the cross of Jesus. This is why affirming the centrality of PSA is so critical—it provides the secure footing from which formation can flourish.
Where the Formation Focus Falters
While Practicing the Way succeeds in motivating readers to live as apprentices of Jesus, the concern arises in what it downplays. Throughout the book, doctrines like sin, wrath, and substitutionary atonement receive little attention, if any. Instead, the emphasis rests almost entirely on imitation and transformation. This imbalance may not be intentional, but it has significant consequences. If readers are taught to pursue the practices of Jesus without grounding them in the saving work of Jesus, they may confuse the fruit of the gospel with its root. Formation then risks becoming disconnected from redemption.
This concern deepens when considering Comer’s broader comments about Penal Substitutionary Atonement. In public remarks, he has at times celebrated scholarship that rejects PSA outright, even calling one critique of it a “knockout blow.”8 Though he later clarified he does not deny substitution altogether, his hesitation speaks volumes. Many who follow him, often with less theological training, may absorb the impression that PSA is an outdated, harsh, or optional part of the Christian faith. Left unchallenged, this can create a generation of disciples who treasure Jesus as example but neglect him as substitute. And without the substitute, the gospel’s power is emptied.
The pastoral danger here cannot be overstated. Spiritual disciplines like prayer, fasting, and Sabbath rest are wonderful gifts—but they do not reconcile us to God. Only the cross does that. To focus on the practices while neglecting the penalty-bearing work of Christ is to place the cart before the horse. Discipleship may appear vibrant for a time, but without the gospel’s foundation, it will eventually grow weary, hollow, or self-centered. True freedom in Christ comes not first from practicing his way, but from trusting in what he accomplished for us. From there, practices become grace-fueled rather than guilt-driven.
Correcting Misunderstandings—PSA Isn’t Novel or Barbaric
For many, objections to Penal Substitutionary Atonement arise from misunderstandings rather than Scripture itself. Some see PSA as a purely Western, modern invention—as if Reformers like Luther and Calvin invented it in the sixteenth century. But the truth is far richer. While the Reformers articulated PSA with fresh clarity, the seeds are woven throughout the church’s history and Scripture itself. From Isaiah’s prophecy of the Suffering Servant who bore our iniquities (Isa. 53:4–6), to Paul’s insistence that Christ was “made sin” for us (2 Cor. 5:21), the reality of substitution is not new but timeless. To call it a novelty is to ignore the long witness of God’s people to his saving work.
Others worry that PSA paints a picture of a violent or angry Father punishing his innocent Son, creating a false division within the Trinity. But the biblical testimony is far different. The Father, Son, and Spirit act in perfect unity to accomplish our salvation. Jesus himself declared that he laid down his life of his own accord, not under compulsion (John 10:17–18). The cross was not divine child abuse—it was the triune God’s loving plan to rescue sinners. Far from dividing the Father and the Son, PSA reveals their united resolve to redeem a lost world.9
Still others fear that PSA excludes or diminishes other atonement motifs, such as Christ’s victory over evil powers (Christus Victor) or his example of sacrificial love. Yet Scripture presents a multifaceted atonement, with PSA at the center. Christ’s bearing of our penalty secures his triumph over Satan (Col. 2:14–15) and inspires our imitation of his love (Eph. 5:1–2). These models do not compete but complement one another, like facets of a diamond reflecting the same light. To neglect PSA, however, is to chip away at the diamond’s core, leaving other motifs without their foundation. Properly understood, PSA doesn’t diminish the richness of the gospel—it unlocks it.
Bringing PSA and Formation Together
The beauty of Penal Substitutionary Atonement is that it doesn’t stand in opposition to spiritual formation—it empowers it. When we know that Jesus has already taken our place, bearing our sin and judgment on the cross, our practices flow from security rather than striving. Prayer, fasting, Sabbath, and service are no longer attempts to earn God’s favor but grateful responses to grace already secured. In this way, PSA fuels formation. It provides the foundation that makes practices life-giving instead of burdensome. Formation without PSA risks burnout, but formation with PSA breathes freedom.
This is where Comer’s passion for apprenticing under Jesus can truly flourish if tethered tightly to the cross. Imagine the power of teaching practices of silence and solitude, not as mere stress management, but as communion with the God who reconciled us through Christ’s blood. Picture the joy of Sabbath, not simply as a productivity hack, but as rest in the finished work of Jesus, who bore our penalty so we could be free. When PSA grounds our practices, they stop being ladders we climb and become gifts we enjoy. They lead us not into self-sufficiency but deeper dependence on grace.
The pastoral task, then, is to unite doctrine and practice, truth and formation, gospel and apprenticeship. If we sever the cross from the practices, we risk creating disciples who look religious but remain unredeemed. If we sever practices from the cross, we risk creating believers who affirm truth but lack transformation. But together—Christ crucified and Christ imitated—we embody the fullness of discipleship. This is what Jesus intended: forgiven sinners, made new, walking daily in rhythms of grace. Formation is vital, but only when it flows from the fountain of substitutionary love.
Conclusion: A Call to Renewed Discipleship
For those drawn to John Mark Comer’s vision of following Jesus, there is much to affirm. His call to slow down, to embrace apprenticeship, and to cultivate rhythms of grace is desperately needed in a restless age. Yet formation, no matter how compelling, cannot save us. Practices can shape us, but they cannot reconcile us to God. That is why Penal Substitutionary Atonement must remain central: because before we could ever walk in the way of Jesus, we needed him to walk to the cross in our place.
The gospel is not first an invitation to imitate, but a proclamation of what has already been accomplished. Christ bore the penalty of sin, satisfying the justice of God so that grace could be freely given.10 From that foundation, the call to formation finds its proper place. We pray, rest, and serve not to earn God’s love but because we already have it. We follow the practices of Jesus because we are forgiven people, not to become forgiven people.
Let us—while embracing discipleship as apprenticeship to Christ—hold fast the gospel’s core: that in Jesus, the wrath we deserved was borne by One who took our place. Spiritual formation and gospel clarity are not alternatives but complementary callings. Let us walk the way of Jesus with confidence, not in our own effort, but in the finished work of the cross. Formation without PSA will always collapse under its own weight, but formation rooted in PSA will flourish in freedom and joy. May we never lose sight of the gospel’s heartbeat: Christ for us, in our place, bearing our sin, and giving us his righteousness. Only then will our apprenticeship to Jesus be both beautiful and true.
John Mark Comer, Practicing the Way (Colorado Springs: WaterBrook, 2024).
Tim Miller, “A Critical Review of John Mark Comer’s Practicing the Way,” Christ Over All, April 1, 2024.
J. I. Packer, “What Did the Cross Achieve? The Logic of Penal Substitution,” Tyndale Biblical Theology Lecture, 1973.
Derek Rishmawy, “Easing Comer’s Fears on Penal Substitution,” The Gospel Coalition, March 20, 2024.
Wayne Grudem, Systematic Theology: An Introduction to Biblical Doctrine (Grand Rapids: Zondervan, 1994), 581–86.
Comer, Practicing the Way.
Ronni Kurtz, “Is This the Way? A Review of Practicing the Way,” Clearly Reformed, March 28, 2024.
Owen Strachan, “John Mark Comer and Penal Substitutionary Atonement,” The Antithesis (Substack), March 19, 2024.
John Owen, The Death of Death in the Death of Christ (1647).
Millard J. Erickson, Christian Theology, 3rd ed. (Grand Rapids: Baker Academic, 2013), 805–10.