An FSMS-Diagnostic Instrument was used to evaluate fifteen Kenyan dairy processors based on indicators and descriptive grids for context riskiness, FSMS activities, and microbial food safety (FS) output with respect to scale of production. Contextual riskiness was diagnosed as low, moderate or high. FSMS activities were diagnosed as absent, basic, average or advanced. FS output was diagnosed as not performed, poor, moderate or good. Four clusters with significantly different (p < 0.05) context riskiness, FSMS activities, and FS output, were identified. Cluster I and II had average context riskiness while cluster III and IV had moderate to high risk. Cluster I had advanced FSMS activities (score 2) while Cluster IV had basic activities. Cluster I had the best food safety output (score 2) while Cluster IV had the most basic activities. Cluster I largely comprised of large scale dairies with FS programs, Cluster II medium scale with FS programs, Cluster III medium scale without FS programs, and Cluster IV small scale dairies without FS programs. The small-scale dairies showed the least performance in validation activities. Medium scale dairies with existing FSMS programs performed least in CCP analysis, extent use of feedback information verification, documentation, and record keeping activities while small and medium scale SME performed poorly in nearly all the FSMS activities apart from the adequacy of physical intervention equipment. In conclusion, small sized dairies are likely to lack an FS program, which increases their contextual risk and therefore their inability to have good performing FSMS or guarantee high microbial safety output of dairy products.