This study aimed to explore the differences in the lipidome and mitochondrial fraction metabolome of Nellore cattle meat in different ranges of ultimate pH (pHu) normal (≤5.79), intermediate (5.80 to 6.19) and high (≥ 6.20) after 3- and 21-d postmortem. Instrumental color, myoglobin redox state, oxygen consumption, and metmyoglobin-reducing activity were measured during storage. A total of 472 lipids and 22 mitochondrial fraction metabolites were identified. Beef with high pHu showed positive regulation of ceramides involved in apoptosis and negative regulation of lipid classes related to membrane permeability and stability. In addition, lower carnitine content was noted in high-pHu beef than in normal-pHu beef. Acylcarnitines, phosphatidylinositol, and IMP showed upregulation in beef with intermediate pHu, indicating changes mainly related to energy, purine and pyruvate metabolism. Aging time impacted on the lipid content and metabolites involved in different metabolic pathways. These results provided new insights into beef's mitochondrial fraction lipid and metabolic profile with different pHu. In addition, beef with intermediate pHu differs from beef with high pHu due to changes in energy metabolism.