This research is oriented to SME’s innovation activities, its management system and competitiveness based on innovations. Research is focused on causalities between innovative controlling, audit, enterprise innovation activities and the results put in context with ROA, ROE, turnover. Data for this research were collected in 317 European SMEs by researches by using questionnaire and analyzed by advanced statistical methods. The aim of this research is to identify key factors for successful innovation enterprise activities, to define weaknesses and common mistakes. Secondary aim is to design controlling process for SME’s innovation activities. The findings of this research are opening up topics for further research.