Summary: This study evaluated the influence of packaging atmosphere (air versus 50% N2/50% CO2) on microbiological (mesophiles, psychrotrophs), physical (gas measurement) and chemical (pH, total volatile basic nitrogen [TVB-N], NH3, H2S and biogenic amines) parameters in freshwater prawns during storage at 0 ± 1 °C for 240 h. To select the most appropriate packaging, 21 batches of each treatment were analysed. Both the packaging permeability and the combination of gases affected the shelf life, but the modified-atmosphere packaging (MAP) was more efficient than air packaging, increasing the shelf life by 40 h. The parameters of pH and TVB-N showed no statistical difference between the two atmosphere conditions all along the storage period. The biogenic amine agmatine showed potential for use as a quality indicator due to the increased concentration during storage. In further studies, this amine can be applied as an indicator for public health issue.