This study evaluated the shelf life of fresh pasta filled with cheese subjected to modified atmosphere packaging (MAP) or air packaging (AP). After a pasteurization treatment, fresh pasta was packaged under a 50/50 N2/CO2 ratio or in air (air batch). Changes in microbial growth, in-package gas composition, chemical—physical parameters and sensory attributes were monitored for 42 days at 4 °C. The pasteurization treatment resulted in suitable microbiological reduction. MAP allowed a mold-free shelf life of the fresh filled pasta of 42 days, whereas air-packaged samples got spoilt between 7 and 14 days. The hurdle approach used (MAP and low storage temperature) prevented the growth of pathogens and alterative microorganisms. MAP samples maintained a high microbiological standard throughout the storage period. The panel judged MAP fresh pasta above the acceptability threshold throughout the shelf life