We performed a quantitative microbiological slaughter process analysis in a large-scale Swiss poultry abattoir. At each of six selected process steps (plucking, cloaca excision, evisceration, washing, water spray chiller and dry air chiller), 103 carcasses from 50 flocks were sampled and quantitatively tested for indicator bacteria (total viable counts, Escherichia (E.) coli/Enterobacteriaceae counts) as well as for Campylobacter spp. and extended-spectrum beta-lactamase-producing Enterobacteriaceae. Samples consisted of a pooled back, breast and leg skin sample as well as swab samples from the thoracic and abdominal cavities. On skin samples, the presence of E. coli and Enterobacteriaceae increased between plucking and evisceration (on average by 1.2 log CFU/g), while washing decreased the microbial load (on average by 0.8 log CFU/g). Subsequent chilling slightly reduced counts on carcasses skin and markedly reduced the counts in the abdominal cavity. ESBL-producing E. coli was present above the limit of detection (LOD) with a prevalence of 6.1%, the majority of which belonged to phylogenetic group A. The bla CTXM-1 gene was found in all ESBL producing strains. The prevalence of Campylobacter above the LOD was 16.7%, and none of the final, chilled carcasses had counts that exceeded 1000 CFU/g. Multilocus sequence typing of 120 Campylobacter jejuni strains yielded 15 different sequence types (ST) among which ST 21 was predominant with 31.7% and four newly defined ST.