This study examines how firms use organizational controls in the knowledge exploitation process to enhance endogenous innovation. Some past studies have shown that controls restrict the flexibility needed in innovation, whereas others have shown that controls enhanced innovation by directing the efforts of research and development professionals. Thus, we extend the theoretical development of organizational control theory to examine how different types of organizational controls (clan, behaviour, and output controls) play different roles at different points in the innovation process. First, we propose that codifying knowledge enhances its level of exploitation, with clan control serving as a moderator. Next, we propose that knowledge exploitation enhances endogenous innovation with behaviour and output controls serving as moderators. Our results from a sample of 607 Chinese manufacturing firms show that clan control moderated the knowledge codification–exploitation relationship positively. Behaviour control moderated the knowledge exploitation–innovation relationship positively, but output control had an inverse U-shaped moderating influence in this relationship. The results indicate that examining different types of organizational controls at different points in the knowledge management process provides a more comprehensive understanding for the role of controls in innovation.