The HACCP/food safety plan is a basic document of every structured food safety management system (FSMS). The aim of the study was to identify and to discuss the most important problems related to the HACCP/food safety plans in 47 small food businesses (SFBs) with standardized FSMSs. Using an affinity diagram, ABCD (Suzuki) method, structured desktop and on-site assessments, the relativization method and Pareto analysis, numerous difficulties and weaknesses were identified, ranked and discussed. This paper presents a unique set of opinions from HACCP/food safety team leaders (HTLs) on the difficulties in the process of developing the HACCP/food safety plans and the weaknesses identified during the on-site assessment of HACCP documentation. Ranking the difficulties by the application of the ABCD (Suzuki) method revealed that in the opinion of HTLs, OPRPs and structured hazard assessment tools, especially in the assessment of the hazard severity, were the most problematic areas in developing HACCP/food safety plans. The Pareto analysis showed that the highest cumulative percentages (almost 60%) of non-compliances occurred in areas of documentation, hazard identification and hazard assessment, process flow diagrams and verification of the system. These findings provide added value to knowledge of the implementation and maintenance of HACCP principles, considerably expanding their range, particularly in regard to SFBs. This will make the results of this study useful for HACCP/food safety teams, official food control inspectors and external experts in strengthening the maintenance of HACCP plans/systems in food businesses with different FSMS models. •The results of assessments of HACCP/food safety plans in small food businesses are presented.•Difficulties and non-compliances in HACCP/food safety plans are ranked and discussed.•The main weaknesses and problems with maintaining HACCP/food safety plans are defined.•An in-deep assessment of HACCP plans in the small businesses sector was carried out.