The available literature lacks information on the metabolic processes taking place in emu muscles after the cessation of circulation. Hence, this study was undertaken to examine the physicochemical characteristics (pH, drip loss, WHC, TBARS, L*, a*, b*) with concomitant changes in protein expression patterns (SDS-PAGE) of femoral muscle (M. iliotibialis lateralis) that occur post mortem and during the first days (0 h, 24 h, 48 h) of its maturation in 1- and 3-year-old emus. Our results indicated that the interaction between emus age and storage time had significant impact on meat pH and all color indicators. Furthermore, we detected 24 differentially expressed protein bands, representing 22 different gene products. ClueGO pathways analysis revealed that these proteins were mainly involved in glycolysis/gluconeogenesis pathway, pyruvate metabolism and pyrophosphate hydrolysis-driven proton transmembrane transporter activity. Based on the results obtained it can be assumed that early post-mortem metabolism of emu muscle is predominantly based on the glycolysis as reflected by the relative abundance alterations of the glycogenolytic and glycolytic enzymes. Moreover, the energy supplies provided by ATP and other high-energy substances degradation is higher in the group of older emus. Our findings also highlighted the complexity of the molecular mechanisms underlying the conversion of muscle to meat.