Abstract Fresh meat color stands as one of the most critical quality indicators influencing consumer perception of meat freshness and purchase decision. Variation in color and color stability among different muscle types exists due to differences in chemical compositions, including lipids and metabolites, and other redox stability-related biochemical properties. Understanding biochemical mechanisms governing color stability in different muscles will offer insights for the industry to develop practical strategies aimed at reducing food waste attributed to discoloration. The objective of the current study was to identify metabolites and lipid compounds potentially linked to oxidative stabilities and relevant biochemical properties across different bovine muscles. Five different muscles [longissimus lumborum (LL), gluteus medius (GM), biceps femoris (BF), semitendinosus (ST), and infraspinatus (IF)] were collected from 16 beef carcasses (USDA Choice) at 2-d postmortem. Multiple cuts were made from each muscle for meat color measurements including instrumental and sensory color evaluations during display, and biochemical attributes, including total reducing activity (TRA), mitochondria-swelling, mitochondrial-lipid oxidation, cytochrome c redox ability (CytC). For the lipidome and metabolome analyses, beef samples were extracted and profiled using non-targeted UPLC-MS analyses. Data analysis was conducted with Metaboanalyst 6.0. The correlation analysis was conduct with Pearson’s correlation and considered the significance level at P < 0.05. In brief, LL and ST maintained greater color stability, redox stability, and lipid/protein oxidative stabilities compared with BF and GM, with IF showing the least (P < 0.05). Also, IF had the greatest levels of mitochondrial-swelling, mitochondrial-lipid oxidation, and oxidized CytC compared with LL (P < 0.05). The ANOVA results found 1,410 significant features in the metabolome analysis and 531 in the lipidome analysis of beef samples. Utilizing partial least square-discriminant analysis (PLS-DA), scatter plots grouped the five muscle types into three distinct clusters: LL and ST, BF and GM, and IF. Pro-apoptotic factors such as phosphatidylserine and lysophosphatidylserine were greater in IF compared with LL and ST (P < 0.05). From the metabolome results, anti-apoptotic factors like creatine and glutathione were increased in LL and ST compared with IF, whereas pro-apoptotic spermidine and adenosine monophosphate (AMP) were greatest in IF (P < 0.05). CIE a* showed a positive correlation with phospholipids and mitochondria-swelling (P < 0.05). Chroma exhibited a positive correlation with TRA, creatine, cyclic AMP, and GMP (P < 0.05). The results suggest that variations in meat color stability among the five beef muscles were likely attributed to differences in the abundance of lipids and metabolites associated with redox and oxidative stabilities, as well as mitochondrial-mediated apoptotic pathways. Specifically, the varying abundance of pro-/anti-apoptotic factors across muscles indicates potential mechanistic biochemical linkages between the apoptosis and meat color. Further research is warranted to investigate the effects of extended aging periods on changes in apoptotic features and color stability of beef muscles.