Value of the Data •The data represents an integrated view of the impact of novel non-thermal processing technologies on fish fillet quality and safety and makes a relevant contribution to the food loss and waste paradigm. •A metagenomics approach for the microbiome used 16s rRNA (bacteria) and internal transcribed spacer (for yeast and fungi) sequencing to provide a global and in-depth overview of microorganism diversity and dynamics in control and HP processed fillets during storage at 2 °C. •SWATH-MS proteomics is used to give insight for the first time into the global impact of HP processing and cold storage on the proteins in sea bass fillets. •The study demonstrates how integration of conventional experimental methods and novel omics technologies corroborate and substantially extend the outcome of previous work. •HP processing is revealed as an emerging processing approach that prolongs the shelf life of highly perishable commodities such as fish fillets.