The broiler supply chain is a complex system that contains several points where foodborne pathogen contamination can occur. Traditionally, broiler research has focused on the risk of Salmonella spp. and Campylobacter spp. contamination. Additionally, research has shown that Listeria spp. could be a pathogen of concern, especially for alternative broiler production systems. Alternative broiler production systems, such as organic or pastured systems, are characterized by alternative rearing practices, such as allowing birds outdoor access. Due to this, food safety risks may be different from those encountered during conventional production. Currently, the food safety risks for alternative production systems are not well characterized. The current study aimed to address knowledge gaps in food safety risks encountered in alternative broiler production and compare those with conventional production. Preharvest and processed broiler samples were collected from pastured poultry farms and processing centers in the southeastern United States. From these data, machine learning models were trained to predict Listeria and Campylobacter prevalence in feces and soil samples based on recent weather patterns. Models with area under the receiver operating characteristic curve (AUC) values of >0.85 were obtained for each pathogen and sample type combination. Additionally, random forest models were constructed to predict Listeria spp. prevalence in pre- and postharvest samples based on farm practice variables. Both models had AUC >0.87. It was found that time of year and broiler age were important predictors of Listeria presence in preharvest samples and that brood feed and processing rinse water chlorination were important predictors in postharvest samples. In the next study, a systematic review and meta-analysis was performed to quantify the differences between conventional and alternative broiler productions systems in Salmonella and Campylobacter prevalence throughout the supply chain. Campylobacter prevalence was significantly higher in alternative environmental samples, but all other comparisons were not significantly different. Finally, a retail-to-consumption risk assessment model was used to compare risks from contaminated broiler meat produced conventionally and alternatively and prepared in-home in the United States. The model estimated that risk was slightly higher for alternatively-processed broiler meat. These results will help in risk-based decision making in the broiler industry.