European food industries are responsible for the safety of the food products brought on the market. Therefore, a legal demanded food safety management system (FSMS) or self-checking system (SCS) is implemented in companies, often based on commercial quality assurance standards as ISO22000, BRC or IFS. The Belgian government provides the possibility for food business operators to have their SCS approved by means of audits conducted by either the competent food safety authority, FASFC, or by a commercial certification body, recognised by the government. The audits are based on specifically developed guides for self-checking per sector, approved by the Belgian government. In view of evaluating the effect of the self-checking system certification on the performance of an implemented FSMS and the companies’ microbiological food safety output, this paper presents the results of an independent self-assessment conducted by eighty-two food business operators in Belgium. The study was conducted in spring/summer of 2010. The outcome of this study is discussed against national inspection results by the FASFC of the year 2009, 2010 and 2011 in Belgian food companies. The enforcement of a SCS by the Belgian government on the performance of a FSMS, their food safety output and their inspection results is less clear for food processing companies compared to the positive effect for the distribution sector. The majority of food processing companies were already certified for a voluntary system next to the legal demanded SCS. No significant difference could be identified between SCS certified and non-certified companies; large, medium or small scale companies and the sector in which they are working for food processing companies. Five clusters could be identified in the performance of a FSMS and microbiological food safety output. In overall Belgian processing companies are having a good performing FSMS and microbiological food safety output.