Conventional pork production, based on highly selected breeds for growth efficiency and carcass leanness, is generally considered to decrease pork quality. In contrast, non-selected breeds produced in extensive systems are associated with high pork quality, which is generally attributed to higher intramuscular fat (IMF) content and less glycolytic muscle metabolism. The present study aimed to determine biochemical, histological and quality traits of loin and ham muscles of pigs from selected Large White (LW) and local French, non-selected Basque (B) breeds. Pigs were reared in a conventional indoor (C, slatted floor), alternative (A, indoor bedding and outdoor area) or extensive system (E, free range, B pigs only). A total of 100 castrated males were produced in 2 replicates, each containing 5 groups of 10 pigs based on breed and system: LWC, LWA, BC, BA and BE. The glycolytic longissimus muscle (LM) and semimembranosus muscle (SM), and the deep red (RSTM) and superficial white (WSTM) portions of semitendinosus muscle (STM) were studied at 145 kg BW. Overall, breed induced stronger effects on muscle traits than the rearing system, among which the E system induced greater changes. The lower muscle growth of B pigs was associated with fewer muscle fibers and a smaller cross-sectional area (CSA) of glycolytic fibers (P < 0.01). The SM was less glycolytic and more oxidative in B than in LW pigs (P < 0.001). The WSTM followed a similar trend, with a larger relative area of type I fibers in B pigs. In contrast, the LM and RSTM were more oxidative in LW pigs. B pigs had higher IMF content and ultimate pH in all muscles, along with lower glycolytic potential, less light and redder meat in the LM and SM (P < 0.001). Compared to the C system, the A system induced only a shift towards a more oxidative metabolism in the LM and a smaller fiber CSA in the RSTM of LW pigs (P < 0.05), without influencing pork quality traits. Compared to BC pigs, BE pigs had a more oxidative and less glycolytic muscle metabolism, along with higher ultimate pH, lower lightness and redder meat (P < 0.01), but similar IMF content. Overall, results indicate that influences of breed and rearing system on muscle properties depend on muscle type, and that IMF content and fiber-type composition are unrelated traits that can be modified independently by genetic or rearing factors.