Poultry bio-mapping helps identify microbial contamination and process optimization opportunities such as sanitary dressing procedures, equipment adjustments, cross-contamination controls, and chemical intervention applications in commercial poultry processing operations. This study focuses on the development of a preliminary microbiological baseline of microbial indicators, including total viable counts (TVC), Enterobacteriaceae (EB), and the quantification and detection of pathogens such as Salmonella and Campylobacter spp. in four commercial broiler processing facilities in Honduras. Whole chicken and wing rinses were collected from four poultry processing plants at different locations: live receiving, rehanger, post-evisceration, post-chiller, and wings. The MicroSnap® system was used for the enumeration of microbial indicators, the BAX®-System-SalQuant® was used for the quantification of Salmonella, and the BAX®-System-CampyQuant™ was used for Campylobacter spp. Negative samples after enumeration were tested with BAX®-System Salmonella and BAX®-System Campylobacter for prevalence analysis, respectively. The TVC and EB counts were continuously reduced from the live receiving to the post-chiller location, presenting a statistically significant increase (p < 0.01) at the wings location. The Salmonella counts were significantly different between stages (p < 0.01). The prevalence of Salmonella was highest in the live receiving stage, with 92.50%, while that at the post-chiller stage was the lowest, at 15.38%. Campylobacter spp. counts were lower than that at the other stages at wings 1.61 Log CFU/sample; however, Campylobacter spp.’s prevalence was higher than 62.5% in all stages. Microbial bio-mapping using novel technologies suitable for mobile applications was conducted in this study to establish statistical process control parameters for microorganisms. A nationwide microbial baseline for commercial broiler processing facilities in Honduras was developed. In-country data serve as a benchmark for continuous improvement at each facility evaluated and can assist regulatory officers in the development of risk-based performance standards aimed at reducing the risk of exposure to consumers.