Managing innovation is vital for many enterprises to survive in a competitive and dynamic environment. Thus, decision-makers have always been involved in the challenge of finding the right performance measures for the innovation process. This paper tackles the issue of innovation performance measurement and management. Its main goal is to present complex results obtained from the Czech manufacturing industry within the research project “Innovation Process Performance Assessment: A Management Control System Approach among Czech Small- and Medium-sized Enterprises” financed by the Czech Science Foundation – 13–20123P. The results reveal many positive aspects of the investigated issue. Czech companies are aware of the importance of innovation and engage in it in various forms. Moreover, the vast majority of the respondents also evaluated the implemented innovations no matter the size of the company. Small- and medium-sized enterprises (SMEs) and large companies differ in terms of their innovation performance measurements and management control techniques and methods. However, both groups adopt traditional measurement tools rather than modern techniques. Here, the gap between global and Czech companies is noted. Therefore, this paper is supposed to motivate researchers to conduct more large-scale studies in the area of innovative performance measurement systems and their implementation in different business sectors and areas.