The aim of this paper was to identify the most important weaknesses in the implementation and effectiveness of the prerequisites and HACCP found in food establishments. To cover these objectives, official control audits of the manuals and their implementation in 1350 small and 66 medium size organizations: restaurants, hotels and cafeterias in one area of the Valencian region (Spain) were carried out from 2007 to 2010. The microbiological quality of 1054 ready-to-consume dishes was also evaluated as an indicator of the effectiveness of the control at Critical Control Points. The results showed that the main deficiencies in the implementation of the prerequisites and HACCP were found in conditions and structural design followed by hygiene & cleaning. Moreover, the analysis of L. monocytogenes in dishes at the time of consumption shows that 99.6% were of good microbiological quality. This indicates that in relation to this hazard, the implementation of safety management systems in the majority of the food establishments was effective. These results demonstrate the crucial role played by official control to ensure the welfare of consumers and how it facilitates continuous improvement in the safety management of these businesses.