Boxes of expanded polystyrene (EPS, with or without ice added), corrugated cardboard (CC, with or without ice added) and polypropylene (PP, gel-ice inside the lid) were used in a case study, for transport of cod loins. Shelf life and quality were analysed after repackaging into modified atmosphere by use of culture dependent microbial methods, analysis of bacterial 16S rRNA sequences, sensory descriptive analysis and analysis of volatile components. The CC boxes showed faster temperature reduction compared to the EPS boxes when no ice added. Still, the microbial shelf life did not differ between transport packaging materials, but adding ice resulted in prolonged microbial shelf life. The sensory shelf lives were similar between all the treatments of MAP, but indications of prolonged sensory shelf life for the CC boxes both with and without ice added, compared to the EPS without ice added, were found. The EPS with added ice compared to the EPS without ice added did also show indication of prolonged sensory shelf life. The PP box seemed to have similar quality preservation as the CC samples with added ice. At the end of shelf life at least two different bacteria genera were detected on the MAP products: Psychrobacter, Shewanella, Carnobacterium, Pseudomonas and/or Acinetobacter. Photobacterium was presented in only minor levels, probably related to inactivation because of freezing. Summarized, this study showed that transport packaging concepts of corrugated cardboard boxes and polypropylene boxes preserved quality equally well as the EPS boxes prior to repackaging and further storage in MAP.