Sous vide cooking implies cooking foods, packed under vacuum conditions, at controlled temperatures (<80 °C). Although this method opens a new window of culinary possibilities, it also involves a series of risks, mainly microbiologically related, that must be assessed. The aim of this work was to evaluate the effectiveness of SV processes to inactivate three important foodborne pathogens (Campylobacter, Salmonella, and Clostridium spores) in chicken breast and eggs (omelet). For this purpose, two levels of inoculation (102 and 106 CFU/g), two different recipes, and two distinct treatments (with and without storage) for each food were studied. After treatments and storage, the corresponding microbiological counts were performed with standard methods. Average inactivation rates observed were 1.70, 4.82, and 4.34 log for Clostridium spores, Campylobacter, and Salmonella, respectively. No significant differences in microbial inactivation were perceived between the different recipes (food composition) or treatments, except for Clostridium spores, which showed a higher inactivation rate (2.30 log) when samples were stored. In general, preliminary results showed that, although appropriate levels of inactivation are reached for vegetative pathogenic cells, in some cases (spores in breast and Salmonella in eggs), the remaining microbiological risks should be considered and further studied, especially if long-term storage is planned.