Traditionally, the microbiological status of meat is determined by culture-based techniques, although many bacteria are not able to grow on conventional media. The aim of this study was to obtain quantitative data on total bacterial cell equivalents, as well as taxa-specific abundances, on carcass surfaces during pig slaughter using quantitative real-time PCR. We evaluated microbial contamination patterns of total bacteria, group, and species throughout slaughtering and on different carcass areas. In addition, we compared contamination levels of breeding sow carcasses with fattening pig carcasses, and we assessed the efficacy of carcass polishing machines under two water amount conditions. Our results demonstrate that relevant meat-spoilage organisms show similar contamination patterns to total bacteria. The highest bacterial load was detected in the stunning chute (4.08 × 10 bacterial cell equivalents per cm) but was reduced by 3 log levels after singeing and polishing ( < 0.001). It increased again significantly by a 4.73-fold change until the classification step. Levels of and species and of followed a similar trend but varied between 0 and 2.49 × 10 bacterial cell equivalents per cm. Microbial levels did not vary significantly between sampled carcass areas for any analyzed taxa. Running the polishing machine with a low water amount proved to be less prone to microbial recontamination compared with a high water amount (17.07-fold change, = 0.024). In the studied slaughterhouse, slaughter of breeding sows did not produce microbiologically safe meat products (>10 cells per cm) and the implementation of specific hazard analysis critical control point systems for the slaughter of breeding sows should be considered. A larger cohort from different abattoirs is needed to confirm our results and determine whether this is universally valid.