This study aimed to evaluate the viability of thermotolerant Campylobacter spp. in chicken carcasses during the slaughter process (n = 150) and at retail level (n = 72). All samples were analysed by quantitative PCR (qPCR), propidium monoazide (PMA)-treated qPCR, and direct plate counting (DPC). The quantitative comparisons were performed for assessing viability and culturability according to the values of the samples that were found to be positive in all methods. Due to the underestimation of viable but unculturable (VBNC) or dead cells, PMA-untreated samples, either at different slaughter stages or at retail level, had a higher positivity and quantity rate (p < 0.05) than the PMA-treated and DPC samples. Across the slaughter line, the above mentioned three methods revealed the highest positivity and quantity level during the evisceration stage. After the water-chilling and storage phases, positivity and quantity rates were not comparable as PMA-qPCR and DPC failed to detect the level of contamination not only in terms of cultivability but also in terms of viability as a result of compromised membrane integrity at low temperatures. In conclusion, recording of Campylobacter spp. during the chicken slaughter process by PMA-treated qPCR would provide more realistic quantitative data for poultry meat contamination.