Chicken meat is considered an important vehicle of foodborne pathogens such as Salmonella spp., demanding an effective control of its contamination during industrial processing. This study aimed to investigate the presence of Salmonella spp. and microbiological indicators at different stages of processing in two slaughterhouses (Sh1, high-capacity; Sh2, low-capacity). Surface samples of chicken carcasses were collected in the following sequential stages: (A) immediately before evisceration, (B) after evisceration, (C) after showering, and (D) after chiller. All samples were submitted for detection of Salmonella spp. and enumeration of mesophilic aerobes, total coliforms, thermotolerant coliforms, and Escherichia coli. The obtained means and frequencies were compared by analysis of variance and chi-square tests (p < 0.05), considering different slaughterhouses and stages of processing. No significant differences were observed between the frequencies of Salmonella spp. obtained at different steps in Sh1 and Sh2 (p > 0.05). Sh2 showed higher levels of microbiological contamination when compared with Sh1 for mesophilic aerobes (in stages B and D), total coliforms and thermotolerant coliforms (stage D), and E. coli (all stages) (p < 0.05). The variation in the levels of contamination by microbiological indicators over the processing indicated the significance of different control procedures adopted by slaughterhouses for the microbiological quality of chicken carcasses.