The pre-slaughter phase of the production process has potentially important animal welfare implications, including mortality (recorded as “Dead on Arrivals”; DOA). To reduce DOA%, specific risk factors need to be identified. DOA% can also be used as a first and quick screening of pre-slaughter broiler welfare under commercial conditions. The aim of the present study was to identify risk factors for DOA% in commercial broiler flocks and to find associations between DOA% and animal-based indicators of broiler welfare during the pre-slaughter phase. Eighty-one transported flocks to five slaughter plants were assessed. Farmers provided information on the flock and observers gathered data on pre-slaughter factors. DOA% was recorded by slaughter plant personnel. The association between risk factors and DOA% was tested using linear mixed models, with slaughter plant as the random effect. Mean (± SE) DOA% was 0.30 ± 0.05% and median was 0.19% (range 0.04 to 3.34%). Two risk factors for DOA% were identified, both related to flock health status during the production phase. Higher DOA% was found when farmers did not check chick quality upon arrival (P = 0.011), although one extreme DOA% caused this significant effect. In addition, on-farm mortality during production (including selective culling) was negatively associated with DOA% (P = 0.011), potentially due to the selective culling on farm. Further research is needed on the impact of on-farm health status on welfare during the pre-slaughter phase, as the current study provided some evidence that on-farm factors are linked to mortality during the pre-slaughter phase. No specific characteristics of the pre-slaughter phase could be identified as risk factor for increased mortality. DOA% was positively associated with five welfare indicators, including indicators of thermal stress, which indicates the potential to use DOA% as a quick, cost-efficient screening tool for those welfare aspects.