Managing fish welfare in captivity is crucial to ensure a sustainable aquaculture production. The physiological stress response, used to evaluate the fish welfare, is universally assessed through the plasma levels of cortisol, glucose and lactate. However, their reliability in cases of long-term chronic stressors has been questioned due to high biological variability and fish adaptation processes. An integrated multi-omics approach (Figure 1) can be a promisor strategy to discover more robust fish welfare biomarkers, since it can offer the possibility of understanding the complete flow of information in the fish biological system. The aim of this work is to use proteomics to identify a restricted protein map as putative fingerprint of fish welfare biomarkers and integrate these results with transcriptomics and metabolomics data to achieve a global picture of the fish response to stress. Sparus aurata was reared under different stressful conditions: overcrowding, repetitive net handling, and hypoxia, using fish reared under optimal conditions for the species as control. Fish were sampled after 45 days of trial and proteins extracts were prepared from liver samples. Proteins were separated by 2D-DIGE and identified by MALDI-TOF/TOF MS. Putative welfare biomarkers were then chosen based on their stress-related function, fold-change and score, and used for primer design. Total RNA was extracted from liver samples using Trizol reagent with DNase treatment and used for cDNA synthesis. The mRNA levels of the target genes were assessed by real-time PCR. Plasma stress markers were measured from blood samples. Comparative proteomics showed, in the liver, a total of 147 proteins with statistically different abundances among conditions, from which 24 were indicated as putative welfare biomarkers and chosen for their transcription level analysis. Quantitative gene expression analysis reveals that the transcripts' levels of 7 of the target genes were modulated. This joint analysis provides a starter point for the development of more reliable fish welfare assessment measures to improve aquaculture sustainability.