Obstacles to innovation often deter or reduce the innovative force within organisations and thereby constitute an important challenge for managers. A vast number of studies analyse the effects of obstacles to innovation but often neglect the individual perspective. This study explores how the operative level and first-level managers in two large R&D organisations perceive innovation obstacles. Moreover, a distinction between the frequency and the effect of obstacles is made by looking not only at which obstacles that are most commonly identified but also linking obstacles to the employees’ innovation self-efficacy. The results reveal that while time-related obstacles are the most frequently identified in both firms, they are not significantly related to a decrease in innovation self-efficacy. In contrast, obstacles referring to organisational culture, failure to set appropriate goals and strategies, as well as poor project portfolio management are significantly connected to lower levels of innovation self-efficacy. The results however differ between the firms and these findings and their implications for theory and practice are discussed in the light of the special characteristics of the two firms.