During the manufacture of Italian salami, a traditional meat product, a sequence of hurdles like meat fermentation, air-drying, and long ripening processes are generally sufficient to inhibit the growth of most pathogens. Furthermore, Italian salami are traditionally produced by adding synthetic nitrates/nitrites to raw meat with safety and technological aims, even if controversial opinions about their use still remain, particularly in relation to the consumer demand for natural food products. In this context, the aim of the study was to investigate the inactivation of Listeria monocytogenes and Salmonella spp. during the manufacturing process of Milano-type salami made with different formulations to evaluate the contribution of the hurdles and the vegetable or synthetic additives on the inactivation of pathogens. Thus, a challenge study was performed dividing ca. 400 kg of Milano-type salami batter into three batches: Batch (A) without nitrates/nitrites; Batch (B) with vegetable nitrates, and Batch (C) with synthetic nitrates/nitrites. The batches were separately inoculated with L. monocytogenes and Salmonella spp. and the pathogens’ survival was evaluated during the fermentation, draining, and 70-day ripening of the Milano-type salami. The pathogen counts decreased in all tested conditions, even though the highest inactivation of L. monocytogenes and Salmonella spp. (p < 0.05) was observed when nitrates or nitrites were added to the batter. This study shows how the safety of these products cannot exclude the aspect of the hurdle technology during the process, which plays a major role in the reduction of pathogens, but additives like nitrates and nitrites allow for a greater margin of safety. Thus, further studies are needed to validate the use of natural compounds as alternatives to conventional preservatives in meat products. These results may provide new information to support food business operators in producing traditional foods with alternative preservatives and competent authorities in verifying the safety of the products made with natural compounds, and to control the process parameters responsible for the synergistic effect against pathogens such as L. monocytogenes and Salmonella spp.