The evolution of innovation ecosystems hinges on the effective coordination between ecosystem leaders and complementors. While ecosystem-sponsored architectural innovations create new technological opportunities for complementors, they may unintentionally disrupt the performance of complementor products that were originally developed based on legacy architectural designs. This study provides empirical evidence of these disruptive effects and explores how complementors’ alignment with the ecosystem leader mitigates such challenges. Focusing on Apple’s release of Core ML—a proprietary artificial intelligence module—in its mobile ecosystem, we employ a difference-in-differences design to investigate variations in complementor performance after adopting this ecosystem-sponsored architectural innovation. Our findings reveal that complementors’ technological and flow alignment with the ecosystem leader is critical for minimizing performance disruptions and enhancing value creation during ecosystem evolution. This study enriches our understanding of architectural changes and complementor heterogeneity in innovation ecosystems.