Microbiological testing is an important quality management tool in the food industry. In this study, the hygiene status of beef carcasses sampled in eight Brazilian slaughterhouses was assessed by enumeration of different hygiene indicator microorganisms, and a model to establish potential associations among these counts was proposed. The carcasses (n = 464) were surface sampled at four slaughtering steps (step 1: Hide after bleeding; step 2: Carcass after hide removal; step 3: Carcass after evisceration; step 4: Carcass after end washing) and subjected to a counting of mesophilic aerobes (MA), Enterobacteriaceae (EB), total coliforms (TC), and Escherichia coli (EC) using PetrifilmTM plates. Among the sampled beef carcasses (step 4), 32 (6.9%) and 71 (15.3%) presented counts above the microbiological criteria established by (EC) No. 1441/2007 for MA and EB, respectively. Thus, indicating that improvements in slaughter hygiene and a review of process controls are demanded in some of the studied slaughterhouses. The log count differences of EC, TC, and EB from MA were considered as response variables as a function of the slaughtering steps. Differential log counts changed consistently with the steps. The measurements, including the patterns in their inherently random variability, were fairly predictable from steps 1 and 4. The results indicated that differential log counts for TC and EC are not relevant, as their concentrations and random pattern can be inferred from counts of MA and EB. The proposed model can be used as a valuable tool for the design and adoption of feasible quality control programs in beef industries. The adoption of such a tool should have a positive contribution on consumers’ health and enhance product quality.