Black truffle (Tuber melanosporum Vitt.) is a fine agro-food product known for its unique aroma and very limited shelf life (maximum of 5–7 days, room temperature). Hypobaric packaging at 30 kPa, a mix of 1% O2/99% N2, and 40% CO2/60% N2 were studied to prolong the shelf life of black truffle at 4 °C in sealed polypropylene vessels, compared to normal atmosphere. Epiphytic microbial population, firmness, weight loss, CO2 formation, and sensory properties were monitored weekly up to 35 days of storage and were related to the volatile profile. Principal components analysis revealed good correlation between the storage time and the decrease of firmness, and the increase of the microbial count and CO2 production. Only truffles stored under hypobaric conditions showed an acceptable quality after 14 days storage. Hypobaric packaging is a cheap strategy to prevent the swelling of vessels caused by respiration and can reduce the deviation from the high-quality level of the fresh product from one to at least two weeks.