Multiple studies have demonstrated atmospheric cold plasma as an effective non-thermal technology for inactivating bacteria, spores, and other microbial contaminants in foods and on non-food surfaces. However, few studies have applied this technique to semi-solid food within a package. This study evaluates the efficacy and the interaction mechanism of high voltage atmospheric cold plasma (HVACP) on Salmonella enterica serovar Typhi (S. enterica) inactivation in agar gels with different compositions. HVACP was generated by a dielectric barrier discharge in air and a modified atmosphere (MA65: 65% O2) in sealed bags. Agar gels of various densities with a pH indicator were inoculated with S. enterica (> 107 cfu) and exposed directly (between the electrode) or indirectly (adjacent to electrode) to 90 kV at 60 Hz for up to 1.5 h. HVACP treatment induced greater than 6 log10 (cfu) reduction in viable bacteria (both with air and MA65) in the plasma penetrated zone exhibiting a pH change. Inactivation of bioluminescent E. coli K12-lux cells in the plasma penetrated zone confirmed that the plasma, and its generated reactive species, inactivates microbes as it penetrates into the gel. A two-minute HVACP treatment resulted in greater than 5 log10 (cfu) S. enterica reduction in applesauce. In summary, these results demonstrate that HVACP can be an effective non-thermal technology to control or even eliminate bacteria populations in semi-solid foods.