Understanding the biochemical changes associated with protein aggregation in meat during storage is critical to improving food safety, quality assurance, and consumer satisfaction in the global meat market. The study evaluated oxygen-induced protein aggregation in the meat of European roe deer (Capreolus capreolus) stored for up to 21 days under refrigeration. Three packaging methods were compared: modified atmosphere packaging with two different gas compositions (MAP(1): 80% O2/20% CO2 and MAP(2): 40% CO2/60% N2) and vacuum packaging (VAC). Additionally, meat dry aging (DA) was included in the study for comparison. Structural proteins most susceptible to aggregation included titin isoform X1 and myosin 1 isoform X1, and among sarcoplasmic proteins, sarcoplasmic/endoplasmic reticulum calcium ATPase 1 isoform X1. In addition, specific proteins involved in aggregate formation under high oxygen conditions were identified, mainly nebulin, isocitrate dehydrogenase, glyceraldehyde phosphate dehydrogenase, and creatine kinase. The extent of their aggregation varied with the type of muscle analyzed, with the most pronounced changes observed in MAP(1) after 21 days. Oxidation plays a crucial role in determining meat quality and shelf life; based on our findings, VAC is recommended for roe deer meat storage.