Kubiak’s QB focus and detail-oriented approach have sharpened San Francisco's offense, making it a balanced, efficient powerhouse, even amidst injuries.
The 49ers entered the season betting big on continuity, and that has paid off with Klay Kubiak as offensive coordinator. More than halfway through the 2025 campaign, it’s clear that Kubiak’s promotion was the right one. Blending the foundational principles of Kyle Shanahan’s system with his own quarterback-focused perspective, Kubiak has helped steer San Francisco’s offense into one of the most balanced, efficient units in the league.
A Lifelong Quarterbacks Coach With a Natural Ascent
Kubiak’s rise through the coaching ranks is a byproduct of the Shanahan coaching tree. But before taking the OC job, he spent years as the 49ers’ quarterbacks coach, praised for his development of young QBs and his calm, detail oriented approach.
That background has shown up this season. Under his direction, the 49ers’ quarterback play has been cleaner, more decisive, and more efficient, especially noticeable when talking about the fact that Mac Jones had to play several games.
Keeping the Shanahan Identity While Adding His Own
Kubiak hasn’t reinvented the wheel, but he has sharpened it.
He doubled down on San Francisco’s signature motion-heavy, timing-based attack while layering in faster tempo looks and more downfield shot opportunities. The result? A unit that is thriving. The run game which has historically been the engine of Shanahan teams has remained both creative and punishing. Even with injury waves that hit the offensive line and skill positions, Kubiak’s weekly adjustments have kept the ground attack efficient and unpredictable.
Developing Young Talent and Stabilizing the Offense Through Injuries
In a season where the 49ers have weathered significant injuries to key playmakers, young contributors have stepped into major roles without the unit losing its rhythm. This is a testament to his teaching style and the clarity of his scheme. Kubiak’s ability to plug in new faces, simplify reads, and exploit matchups has kept San Francisco among the league’s top offenses in yards per play and red-zone efficiency.
A Voice Kyle Shanahan Trusts Completely
Kyle Shanahan’s trust in Kubiak isn’t new but now, it’s fully visible. Kubiak handles more of the week-to-week offensive structure, freeing Shanahan to manage broader game operations and the play calling. Their synergy shows in how seamlessly the offense operates, even in high-stress moments.
Shanahan has repeatedly praised Kubiak’s preparation, player relationships, and deep understanding of the system, calling him “one of the sharpest offensive minds I’ve worked with.”
A Coordinator Whose Impact Is Already Clear
San Francisco promoted Klay Kubiak expecting consistency, growth, and continuity. Halfway through the season, he’s delivered all three. The offense has been steady, explosive when needed, and resilient when challenged.
In a year defined by adversity, Kubiak has been one of the 49ers’ most reliable answers.
Even though Kyle Shanahan remains the primary play caller, Klay Kubiak’s impact on the offense is anything but minimal. Kubiak handled the play calling duties throughout the preseason, giving him valuable reps running the full structure of the offense. Once the regular season began, he shifted into his OC role. The workload is massive even without calling plays on Sundays. He builds the weekly game plan, scripts the opening drives, designs situational packages, oversees quarterback development, helps set protection rules, and manages the constant communication between position groups. In a Shanahan offense, the coordinator isn’t a figurehead, he’s the engine behind the preparation. And Kubiak has been exceptional in that space, ensuring the offense stays detailed, balanced, and ready regardless of who’s on the field.
Thanks for tuning in to my three-part series breaking down all the coordinators shaping the 49ers’ success this season.