The quality assurance of pork meat and products includes the study of factors prior to slaughter such as handling practices, diet and castration, and others during the post-mortem period such as aging, storage, and cooking. The development over the last two decades of high-throughput techniques such as proteomics offer great opportunities to examine the molecular mechanisms and study a priori the proteins in the living pigs and main post-mortem changes and post-translational modifications during the conversion of the muscle into the meat. When the most traditional crossbreeding and rearing strategies to improve pork quality were assessed, the main findings indicate that metabolic pathways early post-mortem were affected. Among the factors, it is well documented that pre-slaughter stress provokes substantial changes in the pork proteome that led to defective meat, and consequently, novel protein biomarkers should be identified and validated. Additionally, modifications in pork proteins had a strong effect on the sensory attributes due to the impact of processing, either physical or chemical. Maillard compounds and protein oxidation should be monitored in order to control proteolysis and volatile compounds. Beyond this, the search of bioactive peptides is becoming a paramount goal of the food and nutraceutical industry. In this regard, peptidomics is a major tool to identify and quantify these peptides with beneficial effects for human health.