This study examines the latent structures and interplay between the constructs employees’ autonomy and innovation capacity in organizations. Using the example of the German manufacturing sector, the question is addressed as to which autonomy-related and innovation-friendly resources are available in companies and which organizational and interactional challenges workers have to face. Methodically, the contribution builds on the explorative approaches of factor and cluster analysis using the BIBB/BAuA employment survey. As a key result, this analysis isolates innovation capacity clusters that divide employees in manufacturing into three groups that give an impression of specific work resources and demands: the potentials (I), the passive balanced (II), and the autonomous front-runners (III). Cluster I describes a group of employees who have little autonomy and face high organizational demands. Their innovation potential is nevertheless high but is hardly ever utilized. Cluster II has generally good working conditions and a balanced relationship between resources and demands, but the innovation-friendly resources are very limited. Cluster III describes the most innovative workers who are very autonomous. However, they run the risk of being crushed under the given organizational pressure. The three clusters provide companies with an opportunity to optimize their innovation capacity.