Background: This study aimed to assess the presence of thermotolerant Campylobacter resistant to ciprofloxacin and erythromycin in poultry slaughterhouses and retail markets, as well as to characterize their multidrug resistance profiles, genetic determinants, and clonal relationships. Methods: Samples were collected at slaughterhouses from cecal content (n = 270), neck skin (n = 270), and wastewater (n = 9), and at retail markets from breast skin (n = 241). Isolates were obtained from mCCDA agar supplemented with ciprofloxacin (2 μg/mL) and identified as C. jejuni or C. coli by PCR. The agar microdilution test was used to determine the minimum inhibitory concentration for ciprofloxacin and erythromycin, and other critical antibiotics. Point mutations in gyrA (Thr86Ile) and 23S rRNA (A2075G), virulence genes (flaA, flhA, cadF, and cdt), and clonal relationships were assessed by PCR and PFGE. Results: At the slaughterhouses, thermotolerant Campylobacter spp. resistant to erythromycin and ciprofloxacin were detected in 48.55% (107/549) of the samples, whereas 4.56% (11/241) of retail samples were positive. The Thr86Ile substitution in gyrA and the A2075G mutation in the 23S rRNA gene were detected in 92.97% and 89.84% of the isolates, respectively. Most isolates (>80%) were multidrug resistant and harbored key virulence genes (flaA, flhA, and cadF). C. jejuni exhibited the highest prevalence of cdt genes (76.19%). There was substantial genotypic diversity among isolates, with broad distribution across the sampled matrices and sites. Conclusions: These findings highlight the circulation of multidrug-resistant and potentially virulent thermotolerant Campylobacter spp. in the later stages of the poultry meat supply chain.