Present hypercompetitive environment and globalization create pressure for competitive environment of SMEs, which need be flexible and operate with high efficiency. SMEs are backbone of European economy and their supporting is main task of any government. It is present challenge to find simple ways how boost SMEs business sector. The controlling as a management tool in its highest implementation maturity level should be for SMEs a key, how to improve processes and move them to position of continuous improvement. Controlling is not only ideal tool for enterprise process auditing, but also has wide scale of managerial usability at operational and strategic management. This paper will be focused on controlling implementation process include main crucial implementation and operating points as controlling implementation level in SME and its influence for SMEs process auditing. The research is connecting quantitative and qualitative research and results will be explained on real SMEs examples. The aim of this paper is finding consequences between SMEs performance and controlling as a management tool in enterprise with focus to process auditing. The research results show us possible ways how to improve SMEs processes to higher level.